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. Author manuscript; available in PMC: 2018 Mar 1.
Published in final edited form as: Cancer Res. 2017 Feb 16;77(5):1051–1059. doi: 10.1158/0008-5472.CAN-16-1336

Table 1.

TME Network resources

Resource Description Status Contact/access
EHS (Engelbreth–Holm–Swarm) sarcoma-derived laminin-rich matrix A pool of EHS ECM for distribution to the cancer research community who work on 3D models to study tumor–host interactions. Available http://tmen.nci.nih.gov/Pages/ResearchResources.aspx
Novel antibodies to detect cancer stem cells and stromal cells This resource consists of validated commercially available antibody reagents for cancer stem cells and stromal cell–specific genes or proteins (biomarkers) that are critical for studying tumor–host interactions. Available http://tmen.nci.nih.gov/Pages/ResearchResources.aspx
Human xenograft tumor bank with characterized stem cell populations A tumor bank of characterized human breast and colon solid tumors containing xenografts. Vials of frozen tumor cells from each tumor type have been stored for use. Available http://tmen.nci.nih.gov/Pages/ResearchResources.aspx
Bone marrow–derived cells from donor mice The BMDC bank contains bone marrow cells from C57BL/6J and C57BL/6-Tg-(UBC-GFP) 30 Scha/J mouse lines in cryopreserved aliquots that can be reinfused as needed. Available http://tmen.nci.nih.gov/Pages/ResearchResources.aspx
RCAS constructs RCAS(A)-GFP: This is an avian retroviral vector for GFP expression in TVa mice. The vector needs to be introduced in DF1 cells for virus generation. Normally, the DF1 cells themselves are introduced into mice directly. RCAS(B)-DsRed: This is an avian retroviral vector for DsRed expression in TVb mice. Available http://tmen.nci.nih.gov/Pages/ResearchResources.aspx
The Matrisome Project Characterizes the in vivo matrisome, i.e., the ensemble of ECM and ECM-associated proteins, in normal tissues and in tumors and predicts bioinformatically the genes encoding the matrisome. Provides details of methods for analyses, an atlas of ECM proteins in diverse tissues and tumors, and incorporates an interactive database with links to external sources. Available http://matrisomeproject.mit.edu
Standard protocol for the characterization of the cellular populations in the TME in human breast cancer The protocol uses IHC on three serial FFPE tissue sections to quantify up to 30 proteins expressed by stromal cells allowing the spatial quantification of subpopulations of stromal cells in a tumor. Available Lisa Coussens (lcoussens@ohsu.edu)
TMEM test TMEM, consisting of direct contact between a macrophage, an endothelial cell, and a tumor cell, is associated with metastasis. TMEM score is predictive of distant metastasis in breast cancer. Available John Condeelis (john.condeelis@einstein.yu.edu)
NANIVID The NANIVID is a multifunctional nanosystem composed of a chemoattractant source (hydrogel-EGF), capsule (cell trap), counter (transparent, interdigitated electrode arrays for sensing cell arrival), and remote reporter (readout electronics). After implanting in a tumor, the device can be retrieved and the cells harvested for subsequent assay. Available John Condeelis (john.condeelis@einstein.yu.edu), James Castracane (jcastracane@sunycnse.com)
HIS A 75-gene panel validated in tumor cells to contain the essential molecules involved in tumor metastasis. The HIS panel has been shown to predict recurrence in breast cancer patients. Available John Condeelis (john.condeelis@einstein.yu.edu)
MenaCalc test A quantitative method of metastasis assessment based on the MenaINV-high/Mena11a-low (MenaCalc) isoform splicing pattern. Available John Condeelis (john.condeelis@einstein.yu.edu)
TMEN-active TMEM-active is a companion diagnostic derived from the known micropharmacology of TMEM function that can be used to assess the pharmacodynamics for drugs designed to inhibit TMEM function. TMEM-active looks at the vascular permeability at TMEM sites that is associated with tumor cell intravasation. Available John Condeelis (john.condeelis@einstein.yu.edu)
Cofilin activity test The cofilin activity test is performed in FFPE tissues to determine the relative levels of cofilin and P-cofilin in breast tumor tissue. Elevated activity levels of the cofilin pathway can lead to tumor cell migration to blood vessels and dissemination via TMEM. Available John Condeelis (john.condeelis@einstein.yu.edu)
Standard protocol for the characterization of the cellular populations in the TME in human melanoma, pancreatic cancer, prostate cancer, and glioblastoma Protocol for the characterization of stromal cells in the TME by flow cytometry using a specific set of well-characterized antibodies Available, validation in progress Melanoma-Jennifer Wargo (JWargo@mdanderson.org); prostate cancer-Kenneth Pienta (kpienta1@jhmi.edu), Raghu Kalluri (RKalluri@mdanderson.org; pancreatic cancer-Michael A. Hollingsworth (mahollin@unmc.edu); glioblastoma-Dolores Hambardzumyan (dolores.hambardzumyan@emory.edu)
RNA sequencing profiling of murine brain microglia and bone marrow–derived macrophages Catalog of differentially expressed transcripts Available Gene Expression Omnibus (GEO) accession numbers GSE46686-GSE46690
RNA sequencing profiling of murine normal resident microglia and low-grade glioma-associated microglia Catalog of differentially expressed transcripts Pending Accession numbers pending, David Gutmann (gutmannd@neuro.wustl.edu)

NOTE: The table lists and describes reagents, methodologies, and devices developed by the TME Network since its creation in 2006, which are available to the scientific community.

Abbreviations: FFPE, formalin-fixed paraffin-embedded; HIS, Human Invasion Signature; NANIVID, NANo IntraVItal Device.