Searching across hundreds of databases

Our searching services are busy right now. Your search will reload in five seconds.

X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

X
Forgot Password

If you have forgotten your password you can enter your email here and get a temporary password sent to your email.

Response and recurrence correlates in individuals treated with neoadjuvant anti-PD-1 therapy for resectable oral cavity squamous cell carcinoma.

Cell reports. Medicine | 2021

Neoadjuvant PD-1 blockade may be efficacious in some individuals with high-risk, resectable oral cavity head and neck cancer. To explore correlates of response patterns to neoadjuvant nivolumab treatment and post-surgical recurrences, we analyzed longitudinal tumor and blood samples in a cohort of 12 individuals displaying 33% responsiveness. Pretreatment tumor-based detection of FLT4 mutations and PTEN signature enrichment favors response, and high tumor mutational burden improves recurrence-free survival. In contrast, preexisting and/or acquired mutations (in CDKN2A, YAP1, or JAK2) correlate with innate resistance and/or tumor recurrence. Immunologically, tumor response after therapy entails T cell receptor repertoire diversification in peripheral blood and intratumoral expansion of preexisting T cell clones. A high ratio of regulatory T to T helper 17 cells in pretreatment blood predicts low T cell receptor repertoire diversity in pretreatment blood, a low cytolytic T cell signature in pretreatment tumors, and innate resistance. Our study provides a molecular framework to advance neoadjuvant anti-PD-1 therapy for individuals with resectable head and neck cancer.

Pubmed ID: 34755131 RIS Download

Research resources used in this publication

None found

Antibodies used in this publication

Associated grants

  • Agency: NCI NIH HHS, United States
    Id: R21 CA215910
  • Agency: NCI NIH HHS, United States
    Id: R21 CA255837
  • Agency: NCI NIH HHS, United States
    Id: R01 CA208514
  • Agency: NCI NIH HHS, United States
    Id: R01 CA175061
  • Agency: NCI NIH HHS, United States
    Id: R01 CA176111
  • Agency: NCI NIH HHS, United States
    Id: P30 CA016042
  • Agency: NCI NIH HHS, United States
    Id: T32 CA009120
  • Agency: NCI NIH HHS, United States
    Id: P01 CA244118
  • Agency: NCATS NIH HHS, United States
    Id: UL1 TR001450
  • Agency: NIDCR NIH HHS, United States
    Id: R21 DE029592
  • Agency: NCI NIH HHS, United States
    Id: P30 CA138313
  • Agency: NCI NIH HHS, United States
    Id: P01 CA168585
  • Agency: NIDCR NIH HHS, United States
    Id: K08 DE026542

Publication data is provided by the National Library of Medicine ® and PubMed ®. Data is retrieved from PubMed ® on a weekly schedule. For terms and conditions see the National Library of Medicine Terms and Conditions.

This is a list of tools and resources that we have found mentioned in this publication.


SAMTOOLS (tool)

RRID:SCR_002105

Original SAMTOOLS package has been split into three separate repositories including Samtools, BCFtools and HTSlib. Samtools for manipulating next generation sequencing data used for reading, writing, editing, indexing,viewing nucleotide alignments in SAM,BAM,CRAM format. BCFtools used for reading, writing BCF2,VCF, gVCF files and calling, filtering, summarising SNP and short indel sequence variants. HTSlib used for reading, writing high throughput sequencing data.

View all literature mentions

CRAN (tool)

RRID:SCR_003005

Network of ftp and web servers around world that store identical, up to date, versions of code and documentation for R. Package archive network for R programming language.

View all literature mentions

Oncotator (tool)

RRID:SCR_005183

A tool for annotating human genomic point mutations and indels with data relevant to cancer researchers. Genomic Annotations, Protein Annotations, and Cancer Annotations are aggregated from many resources. A standalone version of Oncotator is being developed.

View all literature mentions

PRISM (tool)

RRID:SCR_005375

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 5,2022.Tool that predicts interactions between transcription factors and their regulated genes from binding motifs. Understanding vertebrate development requires unraveling the cis-regulatory architecture of gene regulation. PRISM provides accurate genome-wide computational predictions of transcription factor binding sites for the human and mouse genomes, and integrates the predictions with GREAT to provide functional biological context. Together, accurate computational binding site prediction and GREAT produce for each transcription factor: 1. putative binding sites, 2. putative target genes, 3. putative biological roles of the transcription factor, and 4. putative cis-regulatory elements through which the factor regulates each target in each functional role.

View all literature mentions

HTSeq (tool)

RRID:SCR_005514

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software Python package that provides infrastructure to process data from high-throughput sequencing assays. While the main purpose of HTSeq is to allow you to write your own analysis scripts, customized to your needs, there are also a couple of stand-alone scripts for common tasks that can be used without any Python knowledge.

View all literature mentions

PHYLIP (tool)

RRID:SCR_006244

A free package of software programs for inferring phylogenies (evolutionary trees). The source code is distributed (in C), and executables are also distributed. In particular, already-compiled executables are available for Windows (95/98/NT/2000/me/xp/Vista), Mac OS X, and Linux systems. Older executables are also available for Mac OS 8 or 9 systems.

View all literature mentions

Bioconductor (tool)

RRID:SCR_006442

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

View all literature mentions

Promega (tool)

RRID:SCR_006724

An Antibody supplier

View all literature mentions

Image Pro Plus (tool)

RRID:SCR_007369

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software package to capture, process, measure, analyze and share images and data.

View all literature mentions

QIAGEN (tool)

RRID:SCR_008539

A commercial organization which provides assay technologies to isolate DNA, RNA, and proteins from any biological sample. Assay technologies are then used to make specific target biomolecules, such as the DNA of a specific virus, visible for subsequent analysis.

View all literature mentions

BWA (tool)

RRID:SCR_010910

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

View all literature mentions

Abcam (tool)

RRID:SCR_012931

A commercial antibody supplier which supplies primary and secondary antibodies, biochemicals, proteins, peptides, lysates, immunoassays and other kits.

View all literature mentions

FLOWRepository (tool)

RRID:SCR_013779

A database of flow cytometry experiments where users can query and download data collected and annotated according to the MIFlowCyt data standard.

View all literature mentions

Cytobank (tool)

RRID:SCR_014043

A cloud-based platform which allows users to analyze, visualize, and archive multiparamter cytometry data for single-cell biology. Multiple single-cell data sets can be analyzed and visualized simultaneously with a variety of graphics, inlcuding Sunburst, SPADE, and viSNE. Users can store and back up related data such as protocols, microscopy images, and presentations and collaborate and share analysis and data sets with other Cytobank users. Cytobank also provides a variety of services and training sessions to assist with experiment workflow.

View all literature mentions

Sequenza (tool)

RRID:SCR_016662

Software package for copy number estimation from tumor genome sequencing data.Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.

View all literature mentions

CD8 (4B11) (antibody)

RRID:AB_10555292

This monoclonal targets CD8

View all literature mentions

DISCOVERY OmniMap anti-Ms HRP (antibody)

RRID:AB_2885182

This unknown targets IgG, IgM

View all literature mentions

MDM2 (D1V2Z) (antibody)

RRID:AB_2784534

This monoclonal targets MDM2

View all literature mentions

YAP1 antibody [EP1674Y] (antibody)

RRID:AB_2219141

This monoclonal targets YAP1

View all literature mentions

JAK2 antibody [EPR108(2)] (antibody)

RRID:AB_10865183

This monoclonal targets JAK2 antibody [EPR108(2)]

View all literature mentions

PTEN antibody (antibody)

RRID:AB_1241223

This polyclonal targets PTEN

View all literature mentions

Anti-CD278/ICOS (C398.4A)-168Er (antibody)

RRID:AB_2858237

This monoclonal targets CD278/ICOS

View all literature mentions

Anti-Ki-67 (B56)-168Er (antibody)

RRID:AB_2800467

This monoclonal targets Ki-67

View all literature mentions

Anti-Human CD38 (HIT2)-167Er (antibody)

RRID:AB_2802110

This monoclonal targets CD38

View all literature mentions

Anti-Human CD44 (BJ18)-166Er (antibody)

RRID:AB_2744692

This monoclonal targets CD44

View all literature mentions

Anti-Human HLA-DR (L243)-173Yb (antibody)

RRID:AB_2810248

This monoclonal targets HLA-DR

View all literature mentions

Anti-Human CD57 (HCD57)-172Yb (antibody)

RRID:AB_2888930

This monoclonal targets CD57 (HCD57)-172Yb

View all literature mentions

Anti-Human CD62L (DREG-56)-153Eu (antibody)

RRID:AB_2810245

This monoclonal targets CD62L/L-selectin

View all literature mentions

Anti-Human CD45RA (HI100)-143Nd (antibody)

RRID:AB_2651156

This monoclonal targets CD45RA

View all literature mentions

Anti-Human CD11a (HI111)-142Nd (antibody)

RRID:AB_2877095

This monoclonal targets Anti-Human CD11a (HI111)-142Nd

View all literature mentions

Purified anti-human CD26 (antibody)

RRID:AB_314286

This monoclonal targets CD26

View all literature mentions