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Review

Spatial profiling technologies and applications for brain cancers

ORCID Icon, , , ORCID Icon, & ORCID Icon
Pages 323-332 | Received 15 Dec 2020, Accepted 05 Mar 2021, Published online: 19 Mar 2021

References

  • Louis DN, Perry A, Reifenberger G, et al. The 2016 world health organization classification of tumors of the central nervous system: a summary. Acta Neuropathol. 2016 Jun;131(6):803–820. PubMed PMID: 27157931.
  • Ostrom QT, Patil N, Cioffi G, et al. CBTRUS statistical report: primary brain and other central nervous system tumors diagnosed in the United States in 2013–2017. Neuro Oncol. 2020 Oct 30;22(Suppl Supplement_1):iv1–iv96. 22. PubMed PMID: 33123732; PubMed Central PMCID: PMCPMC7596247.
  • Lapointe S, Perry A, Butowski NA. Primary brain tumours in adults. Lancet. 2018 Aug 4;392(10145):432–446. PubMed PMID: 30060998.
  • Sanson M, Marie Y, Paris S, et al. Isocitrate dehydrogenase 1 codon 132 mutation is an important prognostic biomarker in gliomas. J Clin Oncol. 2009 Sep 1;27(25):4150–4154. PubMed PMID: 19636000.
  • Hartmann C, Hentschel B, Wick W, et al. Patients with IDH1 wild type anaplastic astrocytomas exhibit worse prognosis than IDH1-mutated glioblastomas, and IDH1 mutation status accounts for the unfavorable prognostic effect of higher age: implications for classification of gliomas. Acta Neuropathol. 2010 Dec;120(6):707–718. PubMed PMID: 21088844.
  • Cairncross JG, Wang M, Jenkins RB, et al. Benefit from procarbazine, lomustine, and vincristine in oligodendroglial tumors is associated with mutation of IDH. J Clin Oncol. 2014 Mar 10;32(8):783–790. PubMed PMID: 24516018; PubMed Central PMCID: PMCPMC3940537.
  • Brain GBD, Other CNSCC. Global, regional, and national burden of brain and other CNS cancer, 1990–2016: a systematic analysis for the global burden of disease study 2016. Lancet Neurol. 2019 Apr;18(4):376–393. PubMed PMID: 30797715; PubMed Central PMCID: PMCPMC6416167.
  • Bray F, Ferlay J, Soerjomataram I, et al. Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2018 Nov;68(6):394–424. PubMed PMID: 30207593.
  • Gould J. Breaking down the epidemiology of brain cancer. Nature. 2018 Sep;561(7724):S40–S41. PubMed PMID: 30258156.
  • (NBTS) NBtS. quick brain tumour facts 2020 [2020 Oct 6].
  • Achrol AS, Rennert RC, Anders C, et al. Brain metastases. Nat Rev Dis Primers. 2019 Jan 17;5(1):5. PubMed PMID: 30655533.
  • (NCCN) NCCN. NCCN clinical practice guidelines in oncology occult primary version 2 houston. US: TX; A. 2020.
  • Tsukada Y, Fouad A, Pickren JW, et al. Central nervous system metastasis from breast carcinoma autopsy study. Cancer. 1983 Dec 15;52(12):2349–2354. PubMed PMID: 6640506.
  • Posner JB, Chernik NL. Intracranial metastases from systemic cancer. Adv Neurol. 1978;19: 579–592. PubMed PMID:570349.
  • Percy AK. Neoplasms of the central nervous system: epidemiologic considerations. Neurology 1970 Apr;20(4):398–399. PubMed PMID: 5535035..
  • Gaspar L, Scott C, Rotman M, et al. Recursive partitioning analysis (RPA) of prognostic factors in three radiation therapy oncology group (RTOG) brain metastases trials. Int J Radiat Oncol Biol Phys. 1997 Mar 1;37(4):745–751. PubMed PMID: 9128946.
  • Gaspar LE, Scott C, Murray K, et al. Validation of the RTOG recursive partitioning analysis (RPA) classification for brain metastases. Int J Radiat Oncol Biol Phys. 2000 Jul 1;47(4):1001–1006. PubMed PMID: 10863071.
  • Hall WA, Djalilian HR, Nussbaum ES, et al. Long-term survival with metastatic cancer to the brain. Med Oncol. 2000 Nov;17(4):279–286. PubMed PMID: 11114706.
  • Kirkwood JM, Long GV, Trefzer U, et al. BREAK-MB: a phase II study assessing overall intracranial response rate (OIRR) to dabrafenib (GSK2118436) in patients (pts) with BRAF V600E/k mutation-positive melanoma with brain metastases (mets). J clin oncol. 2012;30(15_suppl):8501.
  • Davies MA, Saiag P, Robert C, et al. Dabrafenib plus trametinib in patients with BRAF(V600)-mutant melanoma brain metastases (COMBI-MB): a multicentre, multicohort, open-label, phase 2 trial. Lancet Oncol. 2017 Jul;18(7):863–873. PubMed PMID: 28592387; PubMed Central PMCID: PMCPMC5991615.
  • Long GV, Atkinson V, Lo S, et al. Combination nivolumab and ipilimumab or nivolumab alone in melanoma brain metastases: a multicentre randomised phase 2 study. Lancet Oncol. 2018;19(5):672–681.
  • Peters S, Camidge DR, Shaw AT, et al. Alectinib versus crizotinib in untreated ALK-positive non-small-cell lung cancer. N Engl J Med. 2017 Aug 31;377(9):829–838. PubMed PMID: 28586279.
  • Patel AP, Tirosh I, Trombetta JJ, et al. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014 Jun 20;344(6190):1396–1401. PubMed PMID: 24925914; PubMed Central PMCID: PMCPMC4123637.
  • Arvanitis CD, Ferraro GB, Jain RK. The blood-brain barrier and blood-tumour barrier in brain tumours and metastases. Nat Rev Cancer. 2020 Jan;20(1):26–41. PubMed PMID: 31601988.
  • Vickovic S, Eraslan G, Salmén F, et al. High-definition spatial transcriptomics for in situ tissue profiling. Nature Methods. 2019;16(10):987–990.
  • Jungk C, Mock A, Exner J, et al. Spatial transcriptome analysis reveals Notch pathway-associated prognostic markers in IDH1 wild-type glioblastoma involving the subventricular zone. BMC Med. 2016;14(1):170.
  • Asp M, Bergenstråhle J, Lundeberg J. Spatially resolved transcriptomes—next generation tools for tissue exploration. BioEssays. 2020;42(10):1900221.
  • Klemm F, Maas RR, Bowman RL, et al. Interrogation of the microenvironmental landscape in brain tumors reveals disease-specific alterations of immune cells. Cell. 2020 Jun 25;181(7):1643–1660 e17. PubMed PMID: 32470396.
  • Friebel E, Kapolou K, Unger S, et al. Single-cell mapping of human brain cancer reveals tumor-specific instruction of tissue-invading leukocytes. Cell. 2020 Jun 25;181(7):1626–1642 e20. PubMed PMID: 32470397.
  • Croft PK-D, Chittoory H, Nguyen T, et al. Characterisation of immune cell subsets of tumour infiltrating lymphocytes in brain metastases. bioRxiv. 2021;2021(2):10.430531.
  • Berens ME, Sood A, Barnholtz-Sloan JS, et al. Tumor cell phenotype and heterogeneity differences in IDH1 mutant vs wild-type gliomas. bioRxiv. 2019;690297. 10.1101/690297..
  • Barber H, Lander B, Daniels A, et al. Advanced molecular characterization using digital spatial profiling technology on immuno-oncology targets in methylated compared with unmethylated IDH-wildtype glioblastoma. In: British neuro-oncology society annual meeting. London:Neuro-Oncology Oxford Academic journals; 2019
  • Lein E, Borm LE, Linnarsson SJS. The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing. 2017;358(6359):64–69.
  • Method of the Year. 2020. spatially resolved transcriptomics. Nat Methods. 2021 jan 1 181: 1.
  • Maniatis S, Petrescu J, Phatnani H. Spatially resolved transcriptomics and its applications in cancer. Curr Opin Genet Dev. 2021 Jan 9;66:70–77.
  • Lu Y, Ng A, Kulasekara B, et al. Measuring the spatial whole transcriptome on ffpe specimens using digital spatial profiling: analysis of patients with glioblastoma multiforme treated with neoadjuvant anti-pd1 immunotherapy. In: NanoString Technologies IoSB, editor. 2020.
  • Davidson TB, Lee A, Hsu M, et al. Expression of PD-1 by T cells in malignant glioma patients reflects exhaustion and activation. Clin Cancer Res. 2019 Mar 15 25(6):1913–1922. PubMed PMID: 30498094; PubMed Central PMCID: PMCPMC6420851
  • Goswami S, Walle T, Cornish AE, et al. Immune profiling of human tumors identifies CD73 as a combinatorial target in glioblastoma. Nat Med. 2020 Jan;26(1):39–46. PubMed PMID: 31873309; PubMed Central PMCID: PMCPMC7182038.
  • Toki MI, Merritt C, Ong G, et al. Validation of novel high-plex protein spatial profiling quantitation based on NanoString’s Digital Spatial Profiling (DSP) technology with quantitative fluorescence (QIF). AACR; 2017.
  • Sadeghi Rad H, Bazaz SR, Monkman J, et al. The evolving landscape of predictive biomarkers in immuno-oncology with a focus on spatial technologies. Clin Transl Immunology. 2020;9(11):e1215. PubMed PMID: 33251010; PubMed Central PMCID: PMCPMC7680923.
  • Van TM, Blank CUJI-OT. A user’s perspective on GeoMxTM digital spatial profiling. 1(11–18):2019.
  • Monkman J, Taheri T, Ebrahimi Warkiani M, et al. High-plex and high-throughput digital spatial profiling of non-small-cell lung cancer (NSCLC). Cancers (Basel). 2020 Nov 27;12(12):33261133. PubMed PMID.
  • Baharlou H, Canete NP, Cunningham AL, et al. Mass cytometry imaging for the study of human diseases—applications and data analysis strategies. 2019;10.
  • Mavropolous A, Dongxia L, Ben L Equivalence of imaging mass cytometry and immunofluorescence on FFPE tissue sections.
  • Chang Q, Ornatsky OI, Siddiqui I, et al. Imaging mass cytometry. 2017;91(2):160–169.
  • He B, Bergenstråhle L, Stenbeck L, et al. Integrating spatial gene expression and breast tumour morphology via deep learning. 2020;1-8.
  • Wang Y, Ma S, Ruzzo W. Spatial modeling of prostate cancer metabolic gene expression reveals extensive heterogeneity and selective vulnerabilities. 2020;10(1):1–14.
  • Andersson A, Bergenstrahle J, Asp M, et al. Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography. Commun Biol. 2020 Oct 9;3(1):565. PubMed PMID: 33037292; PubMed Central PMCID: PMCPMC7547664.
  • Duy Pham XT, Jun X, Grice LF, et al. stLearn: integrating spatial location, tissue morphology and gene expression to find cell types, cell-cell interactions and spatial trajectories within undissociated tissues. bioRxiv. 2020. DOI:10.1101/2020.05.31.125658.
  • Maynard KE, Collado-Torres L, Weber LM, et al. Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex. 2020.
  • Maniatis S, Äijö T, Vickovic S, et al. Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis. 2019;364(6435):89–93.
  • Schuerch C, Barlow GL, Bhate SS, et al. Dynamics of the bone marrow microenvironment during leukemic progression revealed by codex hyper-parameter tissue imaging. 2018;132(Supplement 1):935.
  • Rahman A, Jahangir C, Lynch SM, et al. Advances in tissue-based imaging: impact on oncology research and clinical practice. 2020;1-11.
  • Navas T, Fino K, Fung KL, et al. A multiplex immunofluorescence assay to assess immune checkpoint inhibitor-targeted CD8 activation and tumor colocalization in FFPE tissues. American Society of Clinical Oncology; 2019.
  • O’Neil S, Huynh R, Hebert C, et al. editors. Use of Ultivue InSituPlex (R) multiplex immunofluorescence to localize and quantify regulatory T lymphocytes in formalin-fixed paraffin-embedded human tissue sections. JOURNAL FOR IMMUNOTHERAPY OF CANCER. ENGLAND: BMC CAMPUS, 4 CRINAN ST, LONDON N1 9XW; 2019.
  • Sastre AH, Rognoni L, Baehner M, et al. editors. Looking beyond the assay: comparison of multiplex chromogenic and fluorescent immunohistochemistry for standardized immune oncology profiling in non-small cell lung carcinoma patients. JOURNAL FOR IMMUNOTHERAPY OF CANCER. ENGLAND: BMC CAMPUS, 4 CRINAN ST, LONDON N1 9XW; 2019.
  • Liu Y, Zugazagoitia J, Ahmed FS, et al. Immune cell PD-L1 colocalizes with macrophages and is associated with outcome in PD-1 pathway blockade therapy. 2020;26(4):970–977.
  • Chen KH, Boettiger AN, Moffitt JR, et al. Spatially resolved, highly multiplexed RNA profiling in single cells. 2015; 348(6233)
  • Moffitt JR, Hao J, Bambah-Mukku D, et al. High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing. 2016;113(50):14456–14461.
  • Moffitt JR, Bambah-Mukku D, Eichhorn SW, et al. Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. 2018; 362(6416)
  • Xia C, Babcock HP, Moffitt JR, et al. Multiplexed detection of RNA using MERFISH and branched DNA amplification. 2019;9(1):1–13.
  • Buxbaum AR, Haimovich G, Singer R. In the right place at the right time: visualizing and understanding mRNA localization. 2015;16(2):95–109.
  • Die VR. Cellularpatholgie in ihrer Begründung auf physiologische und pathologische Gewebelehre. Hirschwald BA, editor. 1858.
  • Perus LJM, Walsh LA. Microenvironmental heterogeneity in brain malignancies. Front Immunol. 2019;10:2294. PubMed PMID: 31632393; PubMed Central PMCID: PMCPMC6779728.
  • Ajami B, Bennett JL, Krieger C, et al. Local self-renewal can sustain CNS microglia maintenance and function throughout adult life. Nat Neurosci. 2007 Dec;10(12):1538–1543. PubMed PMID: 18026097.
  • Gomez Perdiguero E, Klapproth K, Schulz C, et al. Tissue-resident macrophages originate from yolk-sac-derived erythro-myeloid progenitors. Nature. 2015 Feb 26;518(7540):547–551. PubMed PMID: 25470051; PubMed Central PMCID: PMCPMC5997177.
  • Bowman RL, Klemm F, Akkari L, et al. Macrophage Ontogeny Underlies Differences in Tumor-Specific Education in Brain Malignancies. Cell Rep. 2016 Nov 22;17(9):2445–2459. PubMed PMID: 27840052; PubMed Central PMCID: PMCPMC5450644.
  • Hambardzumyan D, Amankulor NM, Helmy KY, et al. Modeling adult gliomas using RCAS/t-va technology. Transl Oncol. 2009 May;2(2):89–95. PubMed PMID: 19412424; PubMed Central PMCID: PMCPMC2670576.
  • Kalita-de Croft P, Straube J, Lim M, et al. Proteomic analysis of the breast cancer brain metastasis microenvironment. Int J Mol Sci. 2019 May 22;20:10. PubMed PMID: 31121957; PubMed Central PMCID: PMCPMC6567270.
  • Chen Q, Boire A, Jin X, et al. Carcinoma-astrocyte gap junctions promote brain metastasis by cGAMP transfer. Nature. 2016 May 26;533(7604):493–498. PubMed PMID: 27225120; PubMed Central PMCID: PMCPMC5021195.
  • Valiente M, Obenauf AC, Jin X, et al. Serpins promote cancer cell survival and vascular co-option in brain metastasis. Cell. 2014 Feb 27;156(5):1002–1016. PubMed PMID: 24581498; PubMed Central PMCID: PMCPMC3988473.
  • Priego N, Zhu L, Monteiro C, et al. STAT3 labels a subpopulation of reactive astrocytes required for brain metastasis. Nat Med. 2018 Jul;24(7):1024–1035. PubMed PMID: 29892069.
  • Kalita-de Croft P, Lim M, Chittoory H, et al. Clinicopathologic significance of nuclear HER4 and phospho-YAP(S-127) in human breast cancers and matching brain metastases. Ther Adv Med Oncol. 2020 Jul 12 PubMed PMID: WOS:000556975600001; English. DOI:10.1177/1758835920946259..
  • Brastianos PK, Carter SL, Santagata S, et al. Genomic characterization of brain metastases reveals branched evolution and potential therapeutic targets. Cancer Discov. 2015 Nov;5(11):1164–1177. PubMed PMID: 26410082; PubMed Central PMCID: PMCPMC4916970.
  • Puchalski RB, Shah N, Miller J, et al. An anatomic transcriptional atlas of human glioblastoma. Science. 2018 May 11;360(6389):660–663. PubMed PMID: 29748285; PubMed Central PMCID: PMCPMC6414061.
  • Verhaak RG, Hoadley KA, Purdom E, et al. Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010 Jan 19;17(1):98–110. PubMed PMID: 20129251; PubMed Central PMCID: PMCPMC2818769.
  • Venteicher AS, Tirosh I, Hebert C, et al. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science. 2017 Mar 31;355(6332). PubMed PMID: 28360267; PubMed Central PMCID: PMCPMC5519096.
  • Wang Q, Hu B, Hu X, et al. Tumor evolution of glioma-intrinsic gene expression subtypes associates with immunological changes in the microenvironment. Cancer Cell. 2017 Jul 10;32(1):42–56 e6. PubMed PMID: 28697342; PubMed Central PMCID: PMCPMC5599156.
  • Doucette T, Rao G, Rao A, et al. Immune heterogeneity of glioblastoma subtypes: extrapolation from the cancer genome atlas. Cancer Immunol Res. 2013 Aug;1(2):112–122. PubMed PMID: 24409449; PubMed Central PMCID: PMCPMC3881271.
  • Gabrusiewicz K, Rodriguez B, Wei J, et al. Glioblastoma-infiltrated innate immune cells resemble M0 macrophage phenotype. JCI Insight. 2016;1(2). PubMed PMID: 26973881; PubMed Central PMCID: PMCPMC4784261. 10.1172/jci.insight.85841.
  • Neftel C, Laffy J, Filbin MG, et al. An integrative model of cellular states, plasticity, and genetics for glioblastoma. Cell. 2019 Aug 8;178(4):835–849e21. PubMed PMID: 31327527; PubMed Central PMCID: PMCPMC6703186.
  • Jackson HW, Fischer JR, Zanotelli VRT, et al. The single-cell pathology landscape of breast cancer. Nature. 2020 Feb;578(7796):615–620. PubMed PMID: 31959985.
  • McCart Reed AE, Bennett J, Kutasovic JR, et al. Digital spatial profiling application in breast cancer:a user’s perspective. Virchows Arch. 2020 May 26 PubMed PMID: 32458049. 10.1007/s00428-020-02821-9..
  • Stewart RL, Matynia AP, Factor RE, et al. Spatially-resolved quantification of proteins in triple negative breast cancers reveals differences in the immune microenvironment associated with prognosis. Sci Rep. 2020 Apr 20;10(1):6598. PubMed PMID: 32313087; PubMed Central PMCID: PMCPMC7170957.
  • Toki MI, Merritt CR, Wong PF, et al. High-plex predictive marker discovery for melanoma immunotherapy-treated patients using digital spatial profiling. Clin Cancer Res. 2019 Sep 15;25(18):5503–5512. PubMed PMID: 31189645; PubMed Central PMCID: PMCPMC6744974.
  • Amaria RN, Reddy SM, Tawbi HA, et al. Neoadjuvant immune checkpoint blockade in high-risk resectable melanoma. Nat Med. 2018 Nov;24(11):1649–1654. PubMed PMID: 30297909; PubMed Central PMCID: PMCPMC6481682.
  • Blank CU, Rozeman EA, Fanchi LF, et al. Neoadjuvant versus adjuvant ipilimumab plus nivolumab in macroscopic stage III melanoma. Nat Med. 2018 Nov;24(11):1655–1661. PubMed PMID: 30297911.
  • Sadeghi Rad H, Monkman J, Warkiani ME, et al. Understanding the tumor microenvironment for effective immunotherapy. Med Res Rev. 2020 Dec 4 PubMed PMID: 33277742. 10.1002/med.21765..
  • Blomquist MR, Ensign SF, D’Angelo F, et al. Temporospatial genomic profiling in glioblastoma identifies commonly altered core pathways underlying tumor progression. Neurooncol Adv. 2020 Jan-Dec;2(1):vdaa078. PubMed PMID: 32743548; PubMed Central PMCID: PMCPMC7388612.

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