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Last Updated: 02/02/2024

Cancer Immune Monitoring and Analysis Centers (CIMACs) and Cancer Immunologic Data Center (CIDC) Network

The CIMAC-CIDC Network uses harmonized and validated state-of-the-art assays to provide comprehensive immune profiling to identify biomarkers of response, resistance, and toxicity in immunotherapy trials.

The network is building a centralized immuno-oncology (IO) database of biomarker and clinical data from these studies, data from which will be shared with the research community.

CIMAC-CIDC Approaches to Address Challenges in IO Cancer Biomarker Research
Challenge Approach
Complex interplay between cancer and immune system
  • Comprehensive specimen profiling of tumor, tumor microenvironment, blood, and other specimens
Variability in assay performance among labs
Tumor and interpatient heterogeneity
  • Standardized clinical data, specimens, and assays to enable cross-trial analysis
Small size of patient cohorts in clinical trials
  • Larger sample sizes through cross-trial analysis
  • Central database of biomarker and clinical data from multiple trials

HISTORY AND OVERVIEW OF THE CIMAC-CIDC NETWORK

Established in 2017 as part of the Cancer Moonshot Project, the CIMAC-CIDC Network collaborates with clinical trial investigators to design and perform correlative studies in clinical trials of cancer immunotherapy.

The CIMAC-CIDC Network includes:

  • Four CIMAC laboratories at leading cancer research institutions with multidisciplinary groups of doctors and scientists experienced in clinical, translational, and computational research.
  • One CIDC providing the network’s central bioinformatics platform and database of biomarker and clinical data collected from multiple trials.

Overview of CIMAC-CIDC Network published in Clinical Cancer Research

BIOMARKER DISCOVERY

Biomarker and clinical data from CIMAC-CIDC correlative studies in clinical trials of immunotherapy are sent to a central database (CIDC) to enable cross-trial analysis for biomarker discovery.

Diagram depicting the CIMAC-CIDC Network workflow: Biomarker and clinical data from CIMAC-CIDC correlative studies in clinical trials are sent to a central database to enable cross-trial analysis for biomarker discovery.

ORGANIZATION OF THE CIMAC-CIDC NETWORK

CIMACs

This figure describes the workflow and organization of the CIMAC-CIDC network, which is described in more detail in the Clinical Cancer Research publication at https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8491462/

Adapted from Chen et al. Network for Biomarker Immunoprofiling for Cancer Immunotherapy: CIMAC-CIDC, Clin Cancer Res 2021

Graphic showing multiplex immunofluorescence and CyTOF output.
  • Four academic laboratories at leading cancer research institutions perform multi-modal assay analysis in specimens from immunotherapy clinical trials
  • Work with clinical trial investigators to correlate assay data with clinical data in correlative studies, both within and across trials, to identify biomarkers of response, resistance, and toxicity to immunotherapy

CIDC

  • Provides the CIMAC-CIDC Network with its central bioinformatics, IT, and database infrastructure
  • Enables assay and clinical data standardization, develops bioinformatics pipelines, and builds the network’s database
  • Performs the following functions:
    • Collects clinical and biomarker data used in correlative studies, contributing to a growing immuno-oncology database.
    • Standardizes assay data across trials using its centralized, assay-specific pipelines.
    • Facilitates cross-trial analysis of correlative data by collecting a standardized set of clinical data elements across trials.
    • Distributes data to authorized researchers in the network for correlative analysis.
    • Supports activities for sending data to data-sharing repositories such as the Cancer Research Data Commons (CRDC), from which data will be shared with the general research community.

The Clinical Sample Management System (CSMS) tracks and manages specimens among the many network sites.

The Partnership for Accelerating Cancer Therapies (PACT) has collaborated with the CIMAC-CIDC Network since 2018, providing significant financial and scientific support, including additional clinical trials for collaboration with the network. A public-private research collaboration among NIH, FNIH, FDA, and 12 leading pharmaceutical companies, PACT was formed as part of the Cancer Moonshot initiative. Learn more on the FNIH PACT Website External Link .

The terms governing collaborations with the CIMAC-CIDC Network are described in the CIMAC-CIDC Human Material Transfer Agreement (HMTA).

CIMACS AND CIMAC PRINCIPAL INVESTIGATORS

Dana-Farber Cancer Institute

Catherine J. Wu, MD External Link
Chief, Division of Stem Cell Transplantation and Cellular Therapies
Professor of Medicine, Harvard Medical School

Stephen Hodi, MD External Link
Director, Melanoma Center and Center for Immuno-Oncology, Dana-Farber/Brigham and Women’s Cancer Center
Professor of Medicine and Sharon Crowley Martin Chair in Melanoma, Harvard Medical School

Icahn School of Medicine at Mount Sinai

Sacha Gnjatic, PhD External Link
Director, Human Immune Monitoring Center, Mount Sinai
Professor, Hematology and Medical Oncology, and Oncological Sciences, Icahn School of Medicine

Seunghee Kim-Schulze, PhD External Link
Director, Human Immune Monitoring Center, Mount Sinai
Associate Professor, Hematology and Medical Oncology, and Oncological Sciences, Icahn School of Medicine

Stanford University

Holden Maecker, PhD External Link
Professor, Microbiology and Immunology, Stanford University
Director, Human Immune Monitoring Center
Director, Service Centers and Enabling Technologies

Sean Bendall, PhD External Link
Assistant Professor, Pathology, Stanford University

MD Anderson Cancer Center

Ignacio Wistuba, MD External Link
Chair and Professor, Department of Translational Molecular Pathology
Professor, Department of Thoracic/Head and Neck Medical Oncology
Co-Director, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center

Cara Haymaker, PhD
Assistant Professor, Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center

Gheath Alatrash, MD, PhD External Link
Associate Professor, Departments of Stem Cell Transplantation and Cellular Therapy, Hematopoietic Biology and Malignancy, MD Anderson Cancer Center

 

DATA SHARING THROUGH THE NCI CANCER RESEARCH DATA COMMONS (CRDC)

Data from CIMAC-CIDC correlative studies will be placed in the NCI CRDC for sharing with the general research community.

Diagram depicting various data flowing into CIDC from correlative studies, and from CIDC to the NCI Cancer Research Data Commons (CRDC) for sharing with the general research community.

STANDARDIZED ASSAYS

The CIMACs offer comprehensive profiling of specimens using standardized, validated assays. The network has harmonized a core set of these assays to reduce data variability among assay sites, thereby facilitating cross-trial analysis of correlative data. NIH reviewers review and approve all assays for their validation and analytical performance.

To request a copy of CIMAC assay Standard Operating Procedures (SOPs) and validation reports, contact nciCIMACpubs@NIH.gov.

Tissue-imaging assays

  • Multiplex immunofluorescence
  • Multiplex immunohistochemistry
  • Singleplex immunohistochemistry
  • Multiplexed Ion Beam Imaging (MIBI)
  • Spatial transcriptomics (Visium, GeoMx)
  • CODEX

Soluble analyte assays

  • Olink cytokine analysis
  • ELISA Grand Serology

Immune-cell profiling assays

  • Mass Cytometry (CyTOF)
  • EliSPOT

Sequencing assays

  • RNA sequencing
  • Whole Exome Sequencing (WES)
  • NanoString
  • TCRseq (via Adaptive Immunosequencing External Link )
  • ATAC-Seq (epigenomics/regulomics)
  • Circulating tumor DNA (ctDNA) (via The Broad Institute External Link )
  • 16S microbiome sequencing (stool)
  • Single-cell RNA sequencing
  • Single-cell TCR sequencing
  • Single-cell ATAC-Seq
  • Extracellular vesicle small RNA sequencing
  • CITE-seq

 

Key CIMAC-CIDC publications on assay methodology

Assay Harmonization Tumor DNA & RNA Sequencing
Immune Profiling Mass Cytometry
Multiplex Tissue Imaging (IHC/IF)
Assay Methods Tissue imaging Overview
Multiplex immunohistochemistry (IHC)
Multiplex immunofluorescence (IF)
Mass cytometry (CyTOF)

CLINICAL DATA STANDARDIZATION AND SPECIMENS

DownloadTemplate of clinical data elements used in CIMAC-CIDC studies (Excel)

DownloadInstructions for use of template of clinical data elements (Word)

Clinical data elements used in CIMAC-CIDC correlative studies are collected using the template and instructions provided above.

Clinical data elements include the following data for correlation with assay data:

  • Demographics
  • Patient history
  • Disease characteristics
  • Treatment
  • Response
  • Adverse events

Specimen standardization

In their “specimen collection umbrella,” CIMACs describe standardized specimen collections to support multi-assay specimen profiling:

DownloadCIMAC specimen collection umbrella (Word)

CLINICAL TRIALS COLLABORATING WITH CIMAC-CIDC

The CIMAC-CIDC Network collaborates with more than 35 clinical trials of immunotherapy in various cancer disease settings.

Collaborating clinical trials depicted by share of cancer type

Collaborating clinical trials depicted by share of cancer type

Clinical trials with CIMAC-CIDC correlative studies supported by NCI U24 funding:

9204
A Phase I/IB Study of Ipilimumab or Nivolumab in Patients with Relapsed Hematologic Malignancies After Allogeneic Hematopoietic Cell Transplantation

Publication (correlative)

10013
Randomized Phase 2 Study of Neoadjuvant Chemotherapy, Carboplatin and Paclitaxel, with or Without Atezolizumab in Triple Negative Breast Cancer (TNBC)

Publication

10021
A Phase 2 Study of MEDI4736 (Durvalumab) and Tremelimumab Alone or in Combination with High or Low-Dose Radiation in Metastatic Colorectal and NSCLC

Publication (Colorectal Cohort)

Publication (Lung Cohort)

10026
A Phase 1 Study of Ipilimumab in Combination with Decitabine in Relapsed or Refractory Myelodysplastic Syndrome/Acute Myeloid Leukemia

Publication (Clinical results and imaging studies)

Publication (correlative)

10056
A Phase 2 Study of Talimogene Laherparepvec (T-VEC) and Radiation in Localized Soft Tissue Sarcoma

10057
A Phase II Study of Talimogene Laherparepvec Followed by Talimogene Laherparepvec + Nivolumab in Refractory T Cell and NK Cell Lymphomas, Cutaneous Squamous Cell Carcinoma, Merkel Cell Carcinoma, and Other Rare Skin Tumors

10061
A Phase 1 Study of MK-3475 (Pembrolizumab) in Combination with Recombinant Interleukin-12 in Patients with Solid Tumors

10104
A Randomized Phase 2 Study of Cabozantinib in Combination with Nivolumab in Advanced, Recurrent Metastatic Endometrial Cancer

10166
A Phase 2 Study of Atezolizumab and Cobimetinib in PD-1/PD-L1 Inhibitor Resistant or Refractory Non-Small Cell Lung Cancer

10204
A Phase Ib Study of Nivolumab in Patients with Autoimmune Disorders and Advanced Malignancies (AIM-NIVO)

10208
A Phase I Study of Anetumab Ravtansine in Combination with Either Anti-PD-1 Antibody, or Anti-CTLA4 and Anti-PD-1 Antibodies or Anti-PD-1 Antibody and Gemcitabine in Mesothelin-Positive Advanced Pancreatic Adenocarcinoma

10221
A Phase I/II Biomarker Driven Combination Trial of Copanlisib and Immune Checkpoint Inhibitors in Patients with Advanced Solid Tumors

10276
A Phase I/II Study of M3814 and Avelumab in Combination with Hypofractionated Radiation in Patients with Advanced/Metastatic Solid Tumors and Hepatobiliary Malignancies

10300
BLockade of PD-1 Added to Standard Therapy to Target Measurable Residual Disease in Acute Myeloid Leukemia 1 (BLAST MRD AML-1): A Randomized Phase 2 Study of the Anti-PD-1 Antibody Pembrolizumab in Combination with Conventional Intensive Chemotherapy as Frontline Therapy in Patients with Acute Myeloid Leukemia

10334
BLockade of PD-1 Added to Standard Therapy to Target Measurable Residual Disease in Acute Myeloid Leukemia 2 (BLAST MRD AML-2): A Randomized Phase 2 Study of the Venetoclax, Azacitadine, and Pembrolizumab (VAP) Versus Venetoclax and Azacitadine as First Line Therapy in Older Patients with Acute Myeloid Leukemia (AML) Who Are Ineligible or Who Refuse Intensive Chemotherapy

10347
A phase I study with an expansion cohort of duvelisib and nivolumab in mycosis fungoides (MF) and Sézary syndrome (SS)

ABTC-1603
Phase I Study of Neoadjuvant GMCITM plus Immune Checkpoint Inhibitor Combined with Standard of Care for Newly Diagnosed High-Grade Gliomas

E4412
A Phase I Study with an Expansion Cohort/Randomized Phase II Study of the Combinations of Ipilimumab, Nivolumab and Brentuximab Vedotin in Patients with Relapsed/Refractory Hodgkin Lymphoma

EAY131-Z1D
Molecular Analysis for Therapy Choice (MATCH) — MATCH Treatment Subprotocol Z1D: Phase 2 Study of Nivolumab in Patients with Mismatch Repair Deficiency

NRG-GI002
A Phase II Clinical Trial Platform of Sensitization Utilizing Total Neoadjuvant Therapy (TNT) in Rectal Cancer

NRG-GY021
A Phase II Randomized Trial of Olaparib Versus Olaparib Plus Tremelimumab in Platinum-Sensitive Recurrent Ovarian Cancer

NRG-LU004
Phase I Trial of Accelerated or Conventionally Fractionated Radiotherapy Combined with MEDI4736 (Durvalumab) in PD-L1 High Locally Advanced Non-Small Cell Lung Cancer (NSCLC) (ARCHON-1)

PED-CITN-02
GD2-CAR PERSIST: Production and Engineering of GD2-Targeted, Receptor Modified T Cells (GD2CART) for Osteosarcoma or Neuroblastoma to Increase Systemic Tumor Exposure

S1609
DART: Dual Anti-CTLA-4 and Anti-PD-1 Blockade in Rare Tumors

Clinical trials with CIMAC-CIDC correlative studies supported by PACT funding:

14-C-0059G
A Phase I Trial of T Cells Expressing an anti-GD2 Chimeric Antigen Receptor in Children and Young Adults with GD2+ Solid Tumors

2017-0349
A Phase I Study of Nivolumab in Combination with Ipilimumab for the Treatment of Patients with High Risk or Refractory/Relapsed Acute Myeloid Leukemia Following Allogeneic Stem Cell Transplantation

BACCI
BACCI: A Phase II Randomized, Double-Blind, Placebo-Controlled Study of Capecitabine Bevacizumab plus Atezolizumab versus Capecitabine Bevacizumab plus Placebo in Patients with Refractory Metastatic Colorectal Cancer

CA027-005
A Phase 2a Multi-Cohort Trial of Neoadjuvant Nivolumab + BMS-813160 (CCR2/5i) or BMS-986253 (anti-IL-8) for NSCLC or HCC

EA6174
A Phase III Randomized Trial Comparing Adjuvant MK-3475 (Pembrolizumab) to Standard of Care Observation in Completely Resected Merkel Cell Carcinoma

GU16-257
Neoadjuvant gemcitabine, cisplatin, plus nivolumab in patients with muscle-invasive bladder cancer with selective bladder sparing

GU16-287
Randomized phase 2 trial of gemcitabine + carboplatin + nivolumab versus gemcitabine + oxaliplatin + nivolumab in cisplatin-ineligible patients with metastatic urothelial cancer

LuTK02
GMCI plus Standard of Care Immune Checkpoint Inhibitor for Stage III/IV NSCLC Patients

NCT03929029
Neoantigen Vaccine Plus Locally Administered Ipilimumab and Systemic Nivolumab in Advanced Melanoma

OPTIMAL
A Phase II Clinical Trial of Combination Nivolumab (Opdivo), Ipilimumab (Yervoy), and Paclitaxel in Patients With Untreated Metastatic Non-Small Cell Lung Cancer (NSCLC) (The OPTIMAL Trial) [TOP 1705]

S1400I
A Phase III Randomized Study of Nivolumab Plus Ipilimumab Versus Nivolumab for Previously Treated Patients with Stage IV Squamous Cell Lung Cancer and No Matching Biomarker (Lung-Map Sub-Study)

CIMAC-CIDC Network Publications

Correlative studies in clinical trials:

Parra ER, et al. (2024) Multi-omics analysis reveals immune features associated with immunotherapy benefit in squamous cell lung cancer patients from Phase III Lung-MAP S1400I trial. Clin Cancer Res. Epub ahead of print. https://pubmed.ncbi.nlm.nih.gov/38277235

Kaczanowska S, et al. (2023) Immune determinants of CAR-T cell expansion in solid tumor patients receiving GD2 CAR-T cell therapy. Cancer Cell 42(1):35-51.e8. https://pubmed.ncbi.nlm.nih.gov/38134936

Galsky MD, et al. (2023) Gemcitabine and cisplatin plus nivolumab as organ-sparing treatment for muscle-invasive bladder cancer. Nature Medicine 29(11):2825-2834. https://pubmed.ncbi.nlm.nih.gov/37783966

Garcia JS, et al. (2023) Ipilimumab plus decitabine for patients with MDS or AML in post-transplant or transplant naïve settings. Blood 141(15):1884-1888. https://pubmed.ncbi.nlm.nih.gov/36332187

Penter L, et al. (2023) Mechanisms of response and resistance to combined decitabine and ipilimumab for advanced myeloid disease. Blood 141(15):1817-1830. https://pubmed.ncbi.nlm.nih.gov/36706355

Ademuyiwa FO, et al. (2022) A randomized phase 2 study of neoadjuvant carboplatin and paclitaxel with or without atezolizumab in triple negative breast cancer (TNBC) — NCI 10013. NPJ Breast Cancer. 30;8(1):134. https://pubmed.ncbi.nlm.nih.gov/36585404

Schoenfeld JD, et al. (2022) Durvalumab plus tremelimumab alone or in combination with low-dose or hypofractionated radiotherapy in metastatic non-small-cell lung cancer refractory to previous PD(L)-1 therapy: an open-label, multicentre, randomised, phase 2 trial. Lancet Oncol S1470-2045(21)00658-6. https://pubmed.ncbi.nlm.nih.gov/35033226

Zeng Z, Fu J, Cibulskis C, Jhaveri A, Gumbs C, Das B, et al. Cross-Site Concordance Evaluation of Tumor DNA and RNA Sequencing Platforms for the CIMAC-CIDC Network. Clin Cancer Res 27(18):5049-5061. https://pubmed.ncbi.nlm.nih.gov/33323402

Sahaf B, Pichavant M, Lee BH, Duault C, Thrash EM, Davila M, et al. Immune Profiling Mass Cytometry Assay Harmonization: Multicenter Experience from CIMAC-CIDC. Clin Cancer Res 27(18):5062-5071. https://pubmed.ncbi.nlm.nih.gov/34266889

Akturk G, et al. (2021) Multiplex Tissue Imaging Harmonization: A Multicenter Experience from CIMAC-CIDC Immuno-Oncology Biomarkers Network. Clin Cancer Res. 27(18):5072-5083. https://pubmed.ncbi.nlm.nih.gov/34253580

Chen HX, et al. (2021) Network for Biomarker Immunoprofiling for Cancer Immunotherapy: Cancer Immune Monitoring and Analysis Centers and Cancer Immunologic Data Commons (CIMAC-CIDC). Clin Cancer Res. 27(18):5038-5048. https://pubmed.ncbi.nlm.nih.gov/33419780

Monjazeb AM, et al. (2021) A Randomized Trial of Combined PD-L1 and CTLA-4 Inhibition with Targeted Low-Dose or Hypofractionated Radiation for Patients with Metastatic Colorectal Cancer. Clin Cancer Res 27(9). https://pubmed.ncbi.nlm.nih.gov/33568343

Penter L, et al. (2021) Molecular and cellular features of CTLA-4 blockade for relapsed myeloid malignancies after transplantation. Blood 137(23):3212-3217. https://pubmed.ncbi.nlm.nih.gov/33720354/

Additional studies supported by CIMAC-CIDC funding:

2023

2023 Sun, B, et al. Impact of Region-of-Interest Size on Immune Profiling Using Multiplex Immunofluorescence Tyramide Signal Amplification for Paraffin-Embedded Tumor Tissues. Pathobiology. 2023;90(1):1-12. doi: 10.1159/000523751. Epub 2022 May 24. PMID: 35609532.

2023 Steen, CB, et al. Profiling Cellular Ecosystems at Single-Cell Resolution and at Scale with EcoTyper. Methods Mol Biol. 2023;2629:43-71. doi: 10.1007/978-1-0716-2986-4_4. PMID: 36929073.

2023 Rodriguez, S, et al. Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples. J Vis Exp. 2023 Apr 7;(194). doi: 10.3791/64758. PMID: 37092851.

2023 Robinson, ML, et al., Magnitude and kinetics of the human immune cell response associated with severe dengue progression by single-cell proteomics. Sci Adv. 2023 Mar 24;9(12):eade7702. doi: 10.1126/sciadv.ade7702. PMID: 36961888; PMCID: PMC10038348.

2023 Pilcher W, et al. Cross center single-cell RNA sequencing study of the immune microenvironment in rapid progressing multiple myeloma. NPJ Genom Med. 2023 Jan 26;8(1):3. doi: 10.1038/s41525-022-00340-x. PMID: 36702834; PMCID: PMC9879959.

2023 Mao W, et al. A methylation clock model of mild SARS-CoV-2 infection provides insight into immune dysregulation. Mol Syst Biol. 2023 Mar 15:e11361. doi: 10.15252/msb.202211361. PMID: 36919946.

2023 Manning-Geist BL, et al. Phase I Study of a Multivalent WT1 Peptide Vaccine (Galinpepimut-S) in Combination with Nivolumab in Patients with WT1-Expressing Ovarian Cancer in Second or Third Remission. Cancers (Basel). 2023 Feb 25;15(5):1458. doi: 10.3390/cancers15051458. PMID: 36900251; PMCID: PMC10001251.

2023 Malle, L, et al. Autoimmunity in Down's syndrome via cytokines, CD4 T cells and CD11c+ B cells. Nature. 2023 Mar;615(7951):305-314. doi: 10.1038/s41586-023-05736-y. Epub 2023 Feb 22. PMID: 36813963.

2023 Malle L, et al. Autoimmunity in Down's syndrome via cytokines, CD4 T cells and CD11c<sup>+</sup> B cells. Nature. 2023 Mar;615(7951):305-314. doi: 10.1038/s41586-023-05736-y. Epub 2023 Feb 22. PMID: 36813963; PMCID: PMC9945839.

2023 Livanos AE, et al. Anti-Integrin αvβ6 Autoantibodies Are a Novel Biomarker That Antedate Ulcerative Colitis. Gastroenterology. 2023 Apr;164(4):619-629. doi: 10.1053/j.gastro.2022.12.042. Epub 2023 Jan 10. PMID: 36634824.

2023 Kim, YE, et al. Systems biology approaches to unravel lymphocyte subsets and function. Curr Opin Immunol. 2023 Apr 5;82:102323. doi: 10.1016/j.coi.2023.102323. PMID: 37028221.

2023 Francisco-Cruz, A, et al. Analysis of Immune Intratumor Heterogeneity Highlights Immunoregulatory and Coinhibitory Lymphocytes as Hallmarks of Recurrence in Stage I Non-Small Cell Lung Cancer. Mod Pathol. 2023 Jan;36(1):100028. doi: 10.1016/j.modpat.2022.100028. PMID: 36788067.

2023 Esai Selvan M, et al. Germline rare deleterious variant load alters cancer risk, age of onset and tumor characteristics. NPJ Precis Oncol. 2023 Jan 27;7(1):13. doi: 10.1038/s41698-023-00354-3. PMID: 36707626; PMCID: PMC9883433.

2023 Ediriwickrema, A, et al. Single-cell genomics in AML: extending the frontiers of AML research. Blood. 2023 Jan 26;141(4):345-355. doi: 10.1182/blood.2021014670. PMID: 35926108.

2022

2022 Zeng, Z, et al. TISMO: syngeneic mouse tumor database to model tumor immunity and immunotherapy response. Nucleic Acids Res. 2022 Jan 7;50(D1):D1391-D1397. doi: 10.1093/nar/gkab804. PMID: 34534350.

2022 Yaddanapudi K, et al. Single-Cell Immune Mapping of Melanoma Sentinel Lymph Nodes Reveals an Actionable Immunotolerant Microenvironment. Clin Cancer Res. 2022 May 13;28(10) 2069-2081. doi:10.1158/1078-0432.ccr-21-0664. PMID: 35046061; PMCID: PMC9840851.

2022 Vivanco GN, et al. An optimized protocol for phenotyping human granulocytes by mass cytometry. STAR Protoc. 2022 Jun 17;3(2) 101280. doi:10.1016/j.xpro.2022.101280. PMID: 35434655; PMCID: PMC9010787.

2022 Vijayaragavan, K., et al., Single-cell spatial proteomic imaging for human neuropathology. Acta Neuropathol Commun. 2022 Nov 4;10(1):158. doi: 10.1186/s40478-022-01465-x. PMID: 36333818; PMCID: PMC9636771.

2022 Ulicna, L, et al. The Interaction of SWI/SNF with the Ribosome Regulates Translation and Confers Sensitivity to Translation Pathway Inhibitors in Cancers with Complex Perturbations. Cancer Res. 2022 Aug 16;82(16):2829-2837. doi: 10.1158/0008-5472.CAN-21-1360. PMID: 35749589.

2022 Thompson RC, et al. Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae. Nat Med. 2023 Jan;29(1):236-246. doi: 10.1038/s41591-022-02107-4. Epub 2022 Dec 8. PMID: 36482101; PMCID: PMC9873574.

2022 Sigal, N and Maecker, HT. Mass Cytometry Assessment of Cell Phenotypes and Signaling States in Human Whole Blood. Methods Mol Biol. 2022;2543 113-128. doi:10.1007/978-1-0716-2553-8_10. PMID: 36087263; PMCID: PMC9991871.

2022 Schwarz M, et al. Rapid, scalable assessment of SARS-CoV-2 cellular immunity by whole-blood PCR. Nat Biotechnol. 2022 Nov;40(11):1680-1689. doi: 10.1038/s41587-022-01347-6. Epub 2022 Jun 13. PMID: 35697804.

2022 Sand IK, et al. Evaluation of immunological responses to third COVID-19 vaccine among people treated with sphingosine receptor-1 modulators and anti-CD20 therapy. medRxiv [Preprint]. 2022 Jun 14:2022.06.10.22276253. doi: 10.1101/2022.06.10.22276253. Update in: Mult Scler Relat Disord. 2022 Dec 28;70:104486. PMID: 35734083; PMCID: PMC9216728.

2022 Rocha, P, et al. Distinct Immune Gene Programs Associated with Host Tumor Immunity, Neoadjuvant Chemotherapy, and Chemoimmunotherapy in Resectable NSCLC. Clin Cancer Res. 2022 Jun 1;28(11):2461-2473. doi: 10.1158/1078-0432.CCR-21-3207. PMID: 35394499.

2022 Risom T, et al. Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma. Cell. 2022 Jan 20;185(2) 299-310.e18. doi:10.1016/j.cell.2021.12.023. PMID: 35063072; PMCID: PMC8792442.

2022 Penter L, et al. Natural Barcodes for Longitudinal Single Cell Tracking of Leukemic and Immune Cell Dynamics. Front Immunol. 2022 Jan 3;12:788891. doi: 10.3389/fimmu.2021.788891. PMID: 35046946.

2022 Oliveira G, et al. Landscape of helper and regulatory antitumour CD4+ T cells in melanoma. Nature. 2022 May;605(7910):532-538. doi: 10.1038/s41586-022-04682-5. Epub 2022 May 4. PMID: 35508657.

2022 Mortha A, et al. Neutralizing Anti-Granulocyte Macrophage-Colony Stimulating Factor Autoantibodies Recognize Post-Translational Glycosylations on Granulocyte Macrophage-Colony Stimulating Factor Years Before Diagnosis and Predict Complicated Crohn's Disease. Gastroenterology. 2022 Sep;163(3):659-670. doi: 10.1053/j.gastro.2022.05.029. Epub 2022 May 24. PMID: 35623454.

2022 Moore, AR, et al., Gestationally dependent immune organization at the maternal-fetal interface. Cell Rep. 2022 Nov 15;41(7):111651. doi: 10.1016/j.celrep.2022.111651. PMID: 36384130; PMCID: PMC9681661.

2022 Marron TU, et al. Neoadjuvant cemiplimab for resectable hepatocellular carcinoma: a single-arm, open-label, phase 2 trial. Lancet Gastroenterol Hepatol. 2022 Mar;7(3):219-229. doi: 10.1016/S2468-1253(21)00385-X. Epub 2022 Jan 20. PMID: 35065058; PMCID: PMC9901534.

2022 Marmonti, E, et al. Dendritic Cells: The Long and Evolving Road towards Successful Targetability in Cancer. Cells. 2022 Sep 27;11(19):3028. doi: 10.3390/cells11193028. PMID: 36230990. Pathobiology. 2023;90(1):1-12. doi: 10.1159/000523751. Epub 2022 May 24. PMID: 35609532.

2022 Liu, CC, et al., Robust phenotyping of highly multiplexed tissue imaging data using pixel-level clustering. bioRxiv 2022.08.16.504171; doi: https://doi.org/10.1101/2022.08.16.504171

2022 Liu S, et al. Spatial maps of T cell receptors and transcriptomes reveal distinct immune niches and interactions in the adaptive immune response. Immunity. 2022 Oct 11;55(10):1940-1952.e5. doi: 10.1016/j.immuni.2022.09.002. PMID: 36223726.

2022 Liu CC, et al. Reproducible, high-dimensional imaging in archival human tissue by Multiplexed Ion Beam Imaging by Time-of-Flight (MIBI-TOF). Lab Invest. 2022 Jul;102(7) 762-770. doi:10.1038/s41374-022-00778-8. PMID: 35351966.

2022 Lee PC, et al. Reversal of viral and epigenetic HLA class I repression in Merkel cell carcinoma. J Clin Invest. 2022 Jul 1;132(13):e151666. doi: 10.1172/JCI151666. PMID 35775490.

2022 Kim, YE, et al., Expression of terminal deoxynucleotidyl transferase (TdT) identifies lymphoid-primed progenitors in human bone marrow. bioRxiv 2022.10.30.514380; doi: https://doi.org/10.1101/2022.10.30.514380.

2022 Katz Sand I, et al. Evaluation of immunological responses to third COVID-19 vaccine among people treated with sphingosine receptor-1 modulators and anti-CD20 therapy. Mult Scler Relat Disord. 2023 Feb;70:104486. doi: 10.1016/j.msard.2022.104486. Epub 2022 Dec 28. PMID: 36628884; PMCID: PMC9794520.

2022 Karasarides M, et al. Hallmarks of Resistance to Immune-Checkpoint Inhibitors. Cancer Immunol Res. 2022 Apr 1;10(4):372-383. doi: 10.1158/2326-6066.CIR-20-0586. PMID: 35362046

2022 Johnson, B, et al. Phase II study of durvalumab (anti-PD-L1) and trametinib (MEKi) in microsatellite stable (MSS) metastatic colorectal cancer (mCRC). J Immunother Cancer. 2022 Aug;10(8):e005332. doi: 10.1136/jitc-2022-005332 PMID: 36007963.

2022 Glass, MC, et al., Human IL-10-producing B cells have diverse states that are induced from multiple B cell subsets. Cell Rep. 2022 Apr 19;39(3):110728. doi: 10.1016/j.celrep.2022.110728. PMID: 35443184; PMCID: PMC9107325.

2022 Ferrian, S, et al., Single-Cell Imaging Maps Inflammatory Cell Subsets to Pulmonary Arterial Hypertension Vasculopathy. bioRxiv 2022.12.03.518033; doi: https://doi.org/10.1101/2022.12.03.518033.

2022 Dhainaut M, et al. Spatial CRISPR genomics identifies regulators of the tumor microenvironment. Cell. 2022 Mar 31;185(7):1223-1239.e20. doi: 10.1016/j.cell.2022.02.015. Epub 2022 Mar 14. PMID: 35290801; PMCID: PMC8992964.

2022 Chen ST, et al. Shift of lung macrophage composition is associated with COVID-19 disease severity and recovery. bioRxiv [Preprint]. 2022 Jan 12:2022.01.11.475918. doi: 10.1101/2022.01.11.475918. Update in: Sci Transl Med. 2022 Sep 14;14(662):eabn5168. PMID: 35043110; PMCID: PMC8764718.

2022 Chen ST, et al. A shift in lung macrophage composition is associated with COVID-19 severity and recovery. Sci Transl Med. 2022 Sep 14;14(662):eabn5168. doi: 10.1126/scitranslmed.abn5168. Epub 2022 Sep 14. PMID: 36103512.

2022 Carbonell G, et al. Quantitative chest computed tomography combined with plasma cytokines predict outcomes in COVID-19 patients. Heliyon. 2022 Aug;8(8):e10166. doi: 10.1016/j.heliyon.2022.e10166. Epub 2022 Aug 6. PMID: 35958514; PMCID: PMC9356575.

2022 Butler-Laporte G, et al. Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative. PLoS Genet. 2022 Nov 3;18(11):e1010367. doi: 10.1371/journal.pgen.1010367. PMID: 36327219; PMCID: PMC9632827.

2022 Butler-Laporte G, et al. Correction: The dynamic changes and sex differences of 147 immune-related proteins during acute COVID-19 in 580 individuals. Clin Proteomics. 2022 Nov 15;19(1):40. doi: 10.1186/s12014-022-09378-6. Erratum for: Clin Proteomics. 2022 Sep 28;19(1):34. PMID: 36376796; PMCID: PMC9663286.

2022 Baskar, R, et al., Integrating transcription-factor abundance with chromatin accessibility in human erythroid lineage commitment. Cell Rep Methods. 2022 Mar 28;2(3):100188. doi: 10.1016/j.crmeth.2022.100188. Epub 2022 Mar 21. PMID: 35463156; PMCID: PMC9017139.

2022 Baskar, R, et al. Revealing new biology from multiplexed, metal-isotope-tagged, single-cell readouts. Trends Cell Biol. 2022 Jun;32(6):501-512. doi: 10.1016/j.tcb.2022.01.012. PMID: 35181197.

2022 Aranda CJ, et al. IgG memory B cells expressing IL4R and FCER2 are associated with atopic diseases. Allergy. 2023 Mar;78(3):752-766. doi: 10.1111/all.15601. Epub 2022 Dec 19. PMID: 36445014; PMCID: PMC9991991.

2022 Amouzgar M, et al. Supervised dimensionality reduction for exploration of single-cell data by HSS-LDA. Patterns (N Y). 2022 Aug;3(8) 100536. doi:10.1016/j.patter.2022.100536. PMID: 36033591; PMCID: PMC9403402.

2021

2021 Zhang M, et al. Randomized phase II trial of a first-in-human cancer cell lysate vaccine in patients with thoracic malignancies. Transl Lung Cancer Res. 2021 Jul;10(7):3079-3092. doi: 10.21037/tlcr-21-1. PMID: 34430349; PMCID: PMC8350099.

2021 Wong SY, et al.; ICARUS-IBD Working Group. Serologic Response to Messenger RNA Coronavirus Disease 2019 Vaccines in Inflammatory Bowel Disease Patients Receiving Biologic Therapies. Gastroenterology. (2021 Apr 20):S0016-5085(21)00648-X. doi: 10.1053/j.gastro.2021.04.025. Epub ahead of print. PMID: 33887219; PMCID: PMC8055494.

2021 Trinh A, et al. Genomic Alterations during the In Situ to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System. Mol Cancer Res. (2021 Apr);19(4):623-635. doi: 10.1158/1541-7786.MCR-20-0949. Epub 2020 Dec 18. PMID: 33443130; PMCID: PMC8026652.

2021 Thompson RC, et al. Acute COVID-19 gene-expression profiles show multiple etiologies of long-term sequelae. medRxiv [Preprint]. 2021 Oct 5:2021.10.04.21264434. doi: 10.1101/2021.10.04.21264434. PMID: 34642700; PMCID: PMC8509101.

2021 Taing L, et al. CHIPS: A Snakemake pipeline for quality control and reproducible processing of chromatin profiling data. F1000Research 2021 https://f1000research.com/articles/10-517/v1 External Link

2021 Steen CB, et al. The landscape of tumor cell states and ecosystems in diffuse large B cell lymphoma. Cancer Cell. 2021 Oct;39(10) 1422-1437.e10. doi:10.1016/j.ccell.2021.08.011. PMID: 34597589; PMCID: PMC9205168.

2021 Song L, et al. TRUST4: immune repertoire reconstruction from bulk and single-cell RNA-seq data. Nat Methods. 2021 Jun;18(6):627-630. doi: 10.1038/s41592-021-01142-2. Epub 2021 May 13. PMID: 33986545.

2021 Shi Y, et al. Next-Generation Immunotherapies to Improve Anticancer Immunity. Front. Pharmacol 2021 Jan 11;11:566401. doi: 10.3389/fphar.2020.566401. PMID: 33505304.

2021 Penter, L, et al. Longitudinal Single-Cell Dynamics of Chromatin Accessibility and Mitochondrial Mutations in Chronic Lymphocytic Leukemia Mirror Disease History. Cancer Discov. 2021 Dec 1;11(12):3048-3063. doi: 10.1158/2159-8290.CD-21-0276. PMID: 34112698.

2021 Penter L, et al. Coevolving JAK2V617F+relapsed AML and donor T cells with PD-1 blockade after stem cell transplantation: an index case. Blood Adv. 2021 Nov 23;5(22):4701-4709. doi: 10.1182/bloodadvances.2021004335. PMID: 34432868.

2021 Parra ER,et al. Optimization and Validation of Five Automated Multiplex Panels for Immuno-Profiling and Functional Spatial Analysis of Tumor Tissues Using Tyramide Signal Amplification. Sci Rep. (2021 Apr 19);11, Article number: 8511. PMID: 33875760.

2021 Parra ER, et al. Immuno-profiling and cellular spatial analysis using five immune oncology multiplex immunofluorescence panels for paraffin tumor tissue. Sci Rep. 2021 Apr 19;11(1):8511. doi: 10.1038/s41598-021-88156-0. PMID: 33875760; PMCID: PMC8055659.

2021 Parra ER, et al. Identification of distinct immune landscapes using an automated nine-color multiplex immunofluorescence staining panel and image analysis in paraffin tumor tissues. Sci Rep. (2021 Feb 25);11(1):4530. doi: 10.1038/s41598-021-83858-x. PMID: 33633208; PMCID: PMC7907283.

2021 Pachynski RK, et al. IL-7 expands lymphocyte populations and enhances immune responses to sipuleucel-T in patients with metastatic castration-resistant prostate cancer (mCRPC). J Immunother Cancer. 2021 Aug;9(8):e002903. doi: 10.1136/jitc-2021-002903. PMID: 34452927; PMCID: PMC8404457.

2021 Oliveira, G, et al. Phenotype, specificity and avidity of antitumour CD8+ T cells in melanoma. Nature. 2021 Aug;596(7870):119-125. doi: 10.1038/s41586-021-03704-y. Epub 2021 Jul 21. PMID: 34290406.

2021 Luca BA, et al. Atlas of clinically distinct cell states and ecosystems across human solid tumors. Cell. 2021 Oct;184(21) 5482-5496.e28. doi:10.1016/j.cell.2021.09.014. PMID: 34597583; PMCID: PMC8526411.

2021 Lomeli G, et al. Multiplexed Ion Beam Imaging Readout of Single-Cell Immunoblotting. Anal Chem. 2021 Jun 22;93(24):8517-8525. doi: 10.1021/acs.analchem.1c01050. Epub 2021 Jun 9. PMID: 34106685; PMCID: PMC8499019.

2021 Livanos AE, et al. Intestinal Host Response to SARS-CoV-2 Infection and COVID-19 Outcomes in Patients With Gastrointestinal Symptoms. Gastroenterology. 2021 Jun;160(7):2435-2450.e34. doi: 10.1053/j.gastro.2021.02.056. Epub 2021 Mar 4. PMID: 33676971; PMCID: PMC7931673.

2021 Liu, B, et al. The Influence of Increasing Levels of Provider-Patient Discussion on Quit Behavior: An Instrumental Variable Analysis of a National Survey. Int J Environ Res Public Health. 2021 Apr 26;18(9):4593. doi: 10.3390/ijerph18094593. PMID: 33926078.

2021 Laberiano-Fernández C, et al. Best Practices for Technical Reproducibility Assessment of Multiplex Immunofluorescence. Front Mol Biosci. 2021 Aug 31;8:660202. doi: 10.3389/fmolb.2021.660202. PMID: 34532339; PMCID: PMC8438151.

2021 Kumar RG, et al. Development and Validation of a Functionally Relevant Comorbid Health Index in Adults Admitted to Inpatient Rehabilitation for Traumatic Brain Injury. J Neurotrauma. 2022 Jan;39(1-2):67-75. doi: 10.1089/neu.2021.0180. Epub 2021 Nov 24. PMID: 34779252; PMCID: PMC8917887.

2021 Klaeger S, et al. Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples. Mol Cell Proteomics. 2021;20:100133. doi: 10.1016/j.mcpro.2021.100133. Epub 2021 Aug 12. PMID: 34391888.

2021 Kanikarla MP, et al. Pilot Clinical Trial of Perioperative Durvalumab and Tremelimumab in the Treatment of Resectable Colorectal Cancer Liver Metastases. Clin Cancer Res. (2021 Jun 1);27(11):3039-3049. doi: 10.1158/1078-0432.CCR-21-0163. Epub 2021 Apr 2. PMID: 33811152; PMCID: PMC8172528.

2021 Hu Z, et al. Personal neoantigen vaccines induce persistent memory T cell responses and epitope spreading in patients with melanoma. Nat Med. (2021 Mar);27(3):515-525. doi: 10.1038/s41591-020-01206-4. Epub 2021 Jan 21. PMID: 33479501.

2021 Haymaker C, et al. Tilsotolimod with Ipilimumab Drives Tumor Responses in Anti-PD-1 Refractory Melanoma. Cancer Discov. 2021 Aug;11(8):1996-2013. doi: 10.1158/2159-8290.CD-20-1546. Epub 2021 Mar 11. PMID: 33707233.

2021 Hartmann FJ, et al. Single-cell metabolic profiling of human cytotoxic T cells. Nat Biotechnol. (2021 Feb);39(2):186-197. doi: 10.1038/s41587-020-0651-8. Epub 2020 Aug 31. PMID: 32868913; PMCID: PMC7878201.

2021 Greenbaum, S, et al., Spatiotemporal coordination at the maternal-fetal interface promotes trophoblast invasion and vascular remodeling in the first half of human pregnancy. bioRxiv 2021.09.08.459490; doi: https://doi.org/10.1101/2021.09.08.459490.

2021 Gohil SH, et al. Applying high-dimensional single-cell technologies to the analysis of cancer immunotherapy. Nat Rev Clin Oncol. 2021 Apr;18(4):244-256. doi: 10.1038/s41571-020-00449-x. Epub 2020 Dec 4. PMID: 33277626; PMCID: PMC8415132.

2021 Geanon D, et al. A streamlined whole blood CyTOF workflow defines a circulating immune cell signature of COVID-19. Cytometry A (2021 May);99(5):446-461. doi: 10.1002/cyto.a.24317. Epub 2021 Feb 16. PMID: 33496367; PMCID: PMC8013522.

2021 Ferrian S, et al. Multiplexed imaging reveals an IFN-g-driven inflammatory state in nivolumab-associated gastritis. Cell Rep Med. 2021 Oct;2(10) 100419. doi:10.1016/j.xcrm.2021.100419. PMID: 34755133; PMCID: PMC8561237.

2021 Duault C, et al. Activated Natural Killer Cells Predict Poor Clinical Prognosis in High-risk B- and T- cell Acute Lymphoblastic Leukemia. Blood. 2021 Oct 21;138(16) 1465-1480. doi:10.1182/blood.2020009871. PMID: 34077953; PMCID: PMC8532198.

2021 Carbonell G, Del Valle DM, et al. Quantitative chest CT combined with plasma cytokines predict outcomes in COVID-19 patients. medRxiv [Preprint]. 2021 Oct 14:2021.10.11.21264709. doi: 10.1101/2021.10.11.21264709. PMID: 34671777; PMCID: PMC8528085.

2021 Braun DA, et al. Progressive immune dysfunction with advancing disease stage in renal cell carcinoma. Cancer Cell. (2021) May 10;39(5):632-648.e8. doi: 10.1016/j.ccell.2021.02.013. Epub 2021 Mar 11. PMID: 33711273; PMCID: PMC8138872.

2021 Braun DA, et al. Beyond conventional immune-checkpoint inhibition - novel immunotherapies for renal cell carcinoma. Nat Rev Clin Oncol. 2021 Apr;18(4):199-214. doi: 10.1038/s41571-020-00455-z. Epub 2021 Jan 12. PMID: 33437048; PMCID: PMC8317018.

2021 Beckmann ND, et al. Downregulation of exhausted cytotoxic T cells in gene expression networks of multisystem inflammatory syndrome in children. Nat Commun. 2021 Aug 11;12(1):4854. doi: 10.1038/s41467-021-24981-1. PMID: 34381049; PMCID: PMC8357784.

2021 Baranski A, Milo I, Greenbaum S, Oliveria JP, Mrdjen D, Angelo M, Keren L. MAUI (MBI Analysis User Interface)-An image processing pipeline for Multiplexed Mass Based Imaging. PLoS Comput Biol. (2021 Apr 19);17(4):e1008887. doi: 10.1371/journal.pcbi.1008887. PMID: 33872301; PMCID: PMC8084329.

2021 Bannon D, et al. DeepCell Kiosk: scaling deep learning-enabled cellular image analysis with Kubernetes. Nat Methods. (2021 Jan);18(1):43-45. doi: 10.1038/s41592-020-01023-0. Epub 2021 Jan 4. Erratum in: Nat Methods. 2021 Feb;18(2):219. PMID: 33398191.

2021 Bachireddy P, et al. Mapping the evolution of T cell states during response and resistance to adoptive cellular therapy. Cell Rep. 2021 Nov 9;37(6):109992. doi: 10.1016/j.celrep.2021.109992. PMID: 34758319.

2020

2020 Vivanco Gonzalez N, et al. Mass Cytometry Phenotyping of Human Granulocytes Reveals Novel Basophil Functional Heterogeneity. iScience. (2020 Oct 22);23(11):101724. doi: 10.1016/j.isci.2020.101724. PMID: 33205028; PMCID: PMC7653073.

2020 Tsai AG, et al. Multiplexed single-cell morphometry for hematopathology diagnostics. Nat Med 2020 Mar;26(3):408-417. doi: 10.1038/s41591-020-0783-x. Epub 2020 Mar 11. PMID: 32161403.

2020 Sarkizova S, et al. A large peptidome dataset improves HLA class I epitope prediction across most of the human population. Nat Biotechnol 2020 Feb;38(2):199-209. doi: 10.1038/s41587-019-0322-9. Epub 2019 Dec 16. PMID: 31844290.

2020 Sahaf B, et al. High-Parameter Immune Profiling with CyTOF. Methods Mol Biol. 2020;2055:351-368. doi: 10.1007/978-1-4939-9773-2_16. PMID: 31502160; PMCID: PMC7232871.

2020 Leiter A, et al. A Common Pituitary Autoantibody in Two Patients with Immune Checkpoint Inhibitor-Mediated Hypophysitis: ZCCHC8. AACE Clin. Case Rep. (2020 Jul-Aug);6(4): e151-e160. PMID: 32671216

2020 Hartmann FJ, Bendall SC. Immune monitoring using mass cytometry and related high-dimensional imaging approaches. Nat Rev Rheumatol 2020 Feb;16(2):87-99. doi: 10.1038/s41584-019-0338-z. PMID: 31892734.

2020 Gruber CN, et al. Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C). Cell (2020 Nov 12);183(4):982-995.e14. doi: 10.1016/j.cell.2020.09.034. Epub 2020 Sep 14. PMID: 32991843; PMCID: PMC7489877.

2020 Gruber C, et al. Mapping Systemic Inflammation and Antibody Responses in Multisystem Inflammatory Syndrome in Children (MIS-C). medRxiv. (2020) doi:10.1101/2020.07.04.20142752. PMID: 32676612; PMCID: PMC7359537. (Update in: Cell. 2020 Sep 14)

2020 Glass DR, et al. An Integrated Multi-omic Single-Cell Atlas of Human B Cell Identity. Immunity 2020 Jul 14;53(1):217-232.e5. doi: 10.1016/j.immuni.2020.06.013. PMID: 32668225

2020 Gentles AJ, et al. A human lung tumor microenvironment interactome identifies clinically relevant cell-type cross-talk. Genome Biol. (2020 May 7);21(1):107. doi: 10.1186/s13059-020-02019-x. PMID: 32381040; PMCID: PMC7206807.

2020 Fu J, et al. Large-scale public data reuse to model immunotherapy response and resistance. Genome Med 2020 Feb 26;12(1):21. doi: 10.1186/s13073-020-0721-z. PMID: 32102694.

2020 Del Valle DM, et al. An inflammatory cytokine signature predicts COVID-19 severity and death. Nat Med 26, 1636-1643 (2020) August 24. doi.org/10.1038/s41591-020-1051-9. PMID: 32839624.

2020 Braun DA, et al. Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma. Nat Med 2020 Jun;26(6):909-918. doi: 10.1038/s41591-020-0839-y. Epub 2020 May 29.PMID: 32472114.

2020 Beckmann, ND, et al. Cytotoxic lymphocytes are dysregulated in multisystem inflammatory syndrome in children. medRxiv. 2020 Sep 2;2020.08.29.20182899. doi: 10.1101/2020.08.29.20182899. Preprint. PMID: 32909006.

2020 Anandappa AJ, Wu CJ, Ott PA. Directing Traffic: How to Effectively Drive T Cells into Tumors. Cancer Discov. (2020 Feb);10(2):185-197. doi: 10.1158/2159-8290.CD-19-0790. Epub 2020 Jan 23. PMID: 31974169; PMCID: PMC7007384.

2020 Akturk G, et al. Multiplexed Immunohistochemical Consecutive Staining on Single Slide (MICSSS): Multiplexed Chromogenic IHC Assay for High-Dimensional Tissue Analysis. Methods Mol Biol. 2020;2055:497-519. doi: 10.1007/978-1-4939-9773-2_23. PMID: 31502167; PMCID: PMC7869027.

2019

2019 Zhou J, Li J, Guleria I, Chen T, Giobbie-Hurder A, Stevens J, Gupta M, Wu X, Brennick RC, Manos MP, Hodi FS. Immunity to X-linked inhibitor of apoptosis protein (XIAP) in malignant melanoma and check-point blockade. Cancer Immunol Immunother. 2019 Aug;68(8):1331-1340. doi: 10.1007/s00262-019-02370-4. Epub 2019 Jul 18. PMID: 31317218; PMCID: PMC6684401.

2019 Zhang J, et al. Immune receptor repertoires in pediatric and adult acute myeloid leukemia. Genome Med 2019 Nov 26;11(1):73. doi: 10.1186/s13073-019-0681-3. PMID: 31771646.

2019 Salmon H, Remark R, Gnjatic S, Merad M. Host tissue determinants of tumour immunity. Nat Rev Cancer (2019);19(4):215-227. doi: 10.1038/s41568-019-0125-9. PMID: 30867580

2019 Moen E, Bannon D, Kudo T, Graf W, Covert M, Van Valen D. Deep learning for cellular image analysis. Nat Methods 2019 Dec;16(12):1233-1246. doi: 10.1038/s41592-019-0403-1. PMID: 31133758.

2019 Li S, et al. RNase H-dependent PCR-enabled T-cell receptor sequencing for highly specific and efficient targeted sequencing of T-cell receptor mRNA for single-cell and repertoire analysis. Nat Protoc (2019); 14:2571-94. PMID: 31341290.

2019 Lee BH, et al. A Modified Injector and Sample Acquisition Protocol Can Improve Data Quality and Reduce Inter-Instrument Variability of the Helios Mass Cytometer. Cytometry A, (2019); 95(9):1019-1030. doi:10.1002/cyto.a.23866 PMID: 31364278.

2019 Kimmey SC, Borges L, Baskar R, Bendall SC. Parallel analysis of tri-molecular biosynthesis with cell identity and function in single cells. Nat Commun 2019 Mar 12;10(1):1185. doi: 10.1038/s41467-019-09128-7. PMID: 30862852.

2019 Keren L, et al. MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure. Sci Adv 2019 Oct 9;5(10):eaax5851. doi: 10.1126/sciadv.aax5851. eCollection 2019 Oct. PMID: 31633026.

2019 Hu X, et al. Landscape of B cell immunity and related immune evasion in human cancers. Nat Genet 2019 Mar;51(3):560-567. doi: 10.1038/s41588-018-0339-x. Epub 2019 Feb 11. PMID: 30742113.

2019 Hartmann FJ, et al. Scalable Conjugation and Characterization of Immunoglobulins with Stable Mass Isotope Reporters for Single-Cell Mass Cytometry Analysis. Methods Mol Biol 2019;1989:55-81. doi: 10.1007/978-1-4939-9454-0_5. PMID: 31077099.

2019 Hartmann FJ, et al. Comprehensive Immune Monitoring of Clinical Trials to Advance Human Immunotherapy. Cell Rep 2019 Jul 16;28(3):819-831.e4. doi: 10.1016/j.celrep.2019.06.049. PMID: 31315057.

2019 Good Z, et al. Proliferation tracing with single-cell mass cytometry optimizes generation of stem cell memory-like T cells. Nat Biotechnol 2019 Mar;37(3):259-266. doi: 10.1038/s41587-019-0033-2. Epub 2019 Feb 11. PMID: 30742126.

2019 Baskar R, et al. TRAIL-induced variation of cell signaling states provides nonheritable resistance to apoptosis. Life Sci Alliance. 2019 Dec;2(6) e201900554. doi:10.26508/lsa.201900554. PMID: 31704709; PMCID: PMC6848270.

2019 Alatrash G, et al. Fucosylation Enhances the Efficacy of Adoptively Transferred Antigen-Specific Cytotoxic T Lymphocytes. Clin Cancer Res. (2019 Apr 15);25(8):2610-2620. doi: 10.1158/1078-0432.CCR-18-1527. Epub 2019 Jan 15. PMID: 30647079; PMCID: PMC6467811.

2018

2018 Pan D, et al. A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. Science 2018 Feb 16;359(6377):770-775. doi: 10.1126/science.aao1710. Epub 2018 Jan 4. PMID: 29301958.

2018 Miao D, et al. Genomic correlates of response to immune checkpoint therapies in clear cell renal cell carcinoma. Science 2018 Feb 16;359(6377):801-806. doi: 10.1126/science.aan5951. Epub 2018 Jan 4. PMID: 29301960.

2018 Keren L, et al. A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging. Cell 2018 Sep 6;174(6):1373-1387.e19. doi: 10.1016/j.cell.2018.08.039. PMID: 30193111.

2018 Jiang P, et al. Signatures of T cell dysfunction and exclusion predict cancer immunotherapy response. Nat Med 2018 Oct;24(10):1550-1558. doi: 10.1038/s41591-018-0136-1. Epub 2018 Aug 20. PMID: 30127393.

2018 Jiang P, et al. Big Data Approaches for Modeling Response and Resistance to Cancer Drugs. Annul Rev Biomed Data Sic 2018 Jul;1:1-27. doi: 10.1146/annurev-biodatasci-080917-013350. PMID: 31342013.

2018 Hartmann FJ, Simonds EF, Bendall SC. A Universal Live Cell Barcoding-Platform for Multiplexed Human Single Cell Analysis. Sci Rep 2018 Jul 17;8(1):10770. doi: 10.1038/s41598-018-28791-2. PMID: 30018331.

2018 Dobry AS, et al. Management of metastatic melanoma: improved survival in a national cohort following the approvals of checkpoint blockade immunotherapies and targeted therapies. Cancer Immunol Immunother. 2018 Dec;67(12):1833-1844. doi: 10.1007/s00262-018-2241-x. Epub 2018 Sep 6. PMID: 30191256; PMCID: PMC6249064.

2018 Cader FZ, et al. Mass cytometry of Hodgkin lymphoma reveals a CD4 (+) regulatory T-cell-rich and exhausted T-effector microenvironment. Blood 2018 Aug 23;132(8):825-836. doi: 10.1182/blood-2018-04-843714. Epub 2018 Jun 7. PMID: 29880615.