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Single cell RNA sequencing for longitudinal human peripheral blood from HR+ breast cancer patients treated with immunotherapy

ABSTRACT: The limited benefit of immune checkpoint inhibitor in breast cancer indicates the pressing need to identify biomarkers of response to minimize risk and maximize benefit. In this study, we performed single cell RNA sequencing and T cell receptor sequencing on peripheral blood mononuclear cells to monitor the peripheral immune dynamics of an exploratory cohort of hormone receptor positive breast cancer patients treated with neoadjuvant nab-paclitaxel+pembrolizumab with the ultimate goal of identifying potential peripheral blood predictive biomarkers.

ORGANISM(S): Homo sapiens

PROVIDER: GSE300475 | GEO | 2025/07/09

REPOSITORIES: GEO

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Distinct Transcriptional Landscapes Identified by Radiographic Response in Metastatic Triple-Negative Breast Cancer Treated with Carboplatin, Nab-Paclitaxel, and Pembrolizumab in a Single-Arm Phase II Trial

Project description:A single arm, Phase II trial of carboplatin, nab-paclitaxel, and pembrolizumab (CNP) in metastatic triple negative breast cancer (mTNBC) was designed to evaluate overall response rate (ORR), progression-free survival (PFS), duration of response (DOR), safety/tolerability, and identify pathologic and transcriptomic correlates of response to therapy.

2023-10-19 | GSE241876 | GEO

A phase Ib trial evaluating the safety, efficacy, and immunologic effects of pembrolizumab plus paclitaxel or flat-dose capecitabine in 1st/2nd line metastatic triple-negative breast cancer

Project description:Chemoimmunotherapy with anti-programmed cell death 1/ligand 1 and cytotoxic chemotherapy is a promising therapeutic modality for women with triple-negative breast cancer, but questions remain regarding optimal chemotherapy backbone and biomarkers for patient selection. We report final outcomes from a phase Ib trial evaluating pembrolizumab (200mg IV every 3 weeks) with either weekly paclitaxel (80mg/m2 weekly) or flat-dose capecitabine (2000mg orally twice daily for 7 days of every 14-day cycle) in the 1st/2nd line setting. The primary endpoint is safety (receipt of 2 cycles without grade III/IV toxicities requiring discontinuation or ≥21-day delays). The secondary endpoint is efficacy (week 12 objective response). Exploratory aims are to characterize immunologic effects of treatment over time, and to evaluate novel biomarkers. The trial demonstrates that both regimens meet the pre-specified safety endpoint (paclitaxel: 87%; capecitabine: 100%). Objective response rate is 29% for pembrolizumab/paclitaxel (n=4/13, 95% CI: 10-61%) and 43% for pembrolizumab/capecitabine (n=6/14, 95% CI: 18-71%). Partial responses are observed in two subjects with chemo-refractory metaplastic carcinoma (both in capecitabine arm). Both regimens are associated with significant peripheral leukocyte contraction over time. Response is associated with clinical PD-L1 score, non-receipt of prior chemotherapy, and the H&E stromal tumor infiltrating lymphocyte score, but also by a novel 27 gene IO score and spatial biomarkers (lymphocyte spatial skewness). In conclusion, pembrolizumab with paclitaxel or capecitabine is safe and clinically active. Both regimens are lymphodepleting, highlighting the competing immunostimulatory versus lymphotoxic effects of cytotoxic chemotherapy. Further exploration of the IO score and spatial TIL biomarkers is warranted.

2023-02-17 | GSE225078 | GEO

Transcription profiling of human blood from kidney transplant patients to identify biomarkers for early and late stage chronic allograft nephropathy by genomic profiling

Project description:Despite significant improvements in life expectancy of kidney transplant patients due to advances in surgery and immunosuppression, Chronic Allograft Nephropathy (CAN) remains a daunting problem. A complex network of cellular mechanisms in both graft and peripheral immune compartments complicates the non-invasive diagnosis of CAN, which still requires biopsy histology. This is compounded by non-immunological factors contributing to graft injury. There is a pressing need to identify and validate minimally invasive biomarkers for CAN to serve as early predictors of graft loss and as metrics for managing long-term immunosuppression. This study attempts to identify sets of unique transcript biomarkers with high predictive accuracy for both mild and moderate/severe CAN. These biomarkers are the necessary first step to a genomic classification of CAN based on peripheral blood and the targets for a prospective, serial-monitoring clinical study. Experiment Overall Design: We used DNA microarrays and bioinformatics to identify candidate genomic markers of mild and moderate/severe CAN in peripheral blood of two distinct cohorts (n=42 and n=35, respectively) of kidney transplant patients with biopsy-documented histology.

2009-07-19 | E-GEOD-12187 | biostudies-arrayexpress

Peripheral Blood Monocyte Abundance Predicts Outcomes in Breast Cancer Patients

Project description:Biomarkers of response are needed in breast cancer to stratify patients to appropriate therapies and avoid unnecessary toxicity. Peripheral blood gene expression and cell type abundance were used to identify biomarkers of response and recurrence in neoadjuvant chemotherapy treated breast cancer patients. Higher peripheral blood monocyte abundance after neoadjuvant chemotherapy was associated with improved prognosis in multiple independent cohorts of breast cancer patients.

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TNF signature in advanced melanoma patients treated with immune checkpoint inhibitors: results from the MELANFα clinical study

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TIMEPOINT, a phase 1 study of MTL-CEBPA in combination with pembrolizumab, supports the immunomodulatory effect of MTL-CEBPA in solid tumours.

Project description:Many cancer patients don’t benefit from currently-approved immune checkpoint inhibitors (ICI), suggesting that additional immunomodulation of the immunosuppressive tumour microenvironment (TME) is required. MTL-CEBPA specifically upregulates expression of master myeloid transcription factor, CEBPA, relieving myeloid-driven immunosuppression. Here, we report the safety, tolerability, pharmacokinetics, and efficacy of MTL-CEBPA in combination with pembrolizumab in patients with advanced solid tumours that typically show ICI resistance. Multimodal exploratory analyses of paired patient biopsies demonstrate biological changes associated with combination treatment of MTL-CEBPA and pembrolizumab, including increased infiltration of T cell and antigen-presenting cells supporting conversion from an immune desert towards a more immune-inflamed TME. Patients with disease stabilisation demonstrate reductions in immunosuppressive myeloid cells post-treatment. Collectively, these data support a role for MTL-CEBPA in reducing immunosuppression in the TME. This study was registered at ClinicalTrials.gov (NCT04105335). This manuscript also reports proteomic data from patients treated with MTL-CEBPA in combination with sorafenib from clinical trial, OUTREACH, accessible at ClinicalTrials.gov, number NCT02716012 and reported. Stored plasma from patients from this clinical trial were analysed using OLINK as described below.

2025-05-07 | PXD060726 | Pride

Biomarkers for Early and Late Stage Chronic Allograft Nephropathy by Genomic Profiling of Peripheral Blood

2009-07-13 | GSE12187 | GEO

Homo sapiens

Project description:Peripheral blood biomarkers in Friedreich's ataxia

| PRJNA396198 | ENA

Expression data from human patients with slow or rapid Parkinson's Disease progression

Project description:Parkinson’s Disease is a multi-system, disabling progressive neurodegenerative condition. Clinical progression is highly heterogeneous and, thus far, there are not available biomarkers to accurately predict the rate of disease progression. Thus, identifying molecular signatures that allow discriminating between different progression rates might significantly assist the therapeutic strategy, and enable improved outcomes in clinical trials. We performed an exploratory cross-sectional study aimed at determining whether gene expression differences in peripheral blood may be used to discriminate between patients with slow or rapid Parkinson’s disease progression

2016-04-25 | GSE80599 | GEO

Evaluation of a novel clinical platform for cardiovascular drug development

Project description:Objectives M-bM-^@M-^STo determine whether inflammation biomarkers can be used as indicators of therapeutic response, an exploratory study was performed to ascertain whether short term improvements in risk parameters will have measureable effects on a pre-defined panel of plaque inflammation biomarkers. Methods and Results M-bM-^@M-^S Patients (n=121) with peripheral arterial disease were enrolled into one of three sub-studies based upon the presence of hypercholesterolemia, hypertension, or diabetes. Patients were randomized to 6 weeks of drug treatment vs. placebo and underwent catheter excision of atherosclerotic tissue from one extremity at baseline and the contralateral extremity after treatment. Simvastatin 40mg once daily reduced LDL-C by 43% (p<0.01), losartan 50mg once daily reduced diastolic blood pressure by 4 mm Hg (p=0.099), and pioglitazone 30mg once daily reduced serum glucose by 66mg/dL (p=0.008). Despite these effects, there were no consistent treatment effects on a large panel of plaque protein, RNA and lipid biomarkers. Conclusions M-bM-^@M-^S Short term treatment with drugs that improve cardiovascular risk parameters did not result in a measureable reduction in the levels of peripheral arterial plaque inflammation biomarkers. Further studies are required to identify biomarkers that are sufficiently predictive to be used to identify drug candidates for testing in large cardiovascular outcome studies. (ClinicalTrials.gov: NCT00720577) Human peripheral atherosclerosis plaque was extracted from lower extremities, and RNA, lipids and proteins extracted. RNA was analyzed in an Agilent two-color platform.

2012-05-15 | E-GEOD-37824 | biostudies-arrayexpress

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