This is a prospective study of newly diagnosed triple negative breast cancer (TNBC)
patients undergoing standard of care neoadjuvant chemotherapy and correlate gut and
intratumoral microbiome composition and anti-tumor immune responses with pCR.
The biopsy at diagnosis will be used as a pretreatment control for the assessment of
TILs, PD-L1 expression, immune signature profiles. Both tumor and "normal" adjacent
non-tumor tissue will be evaluated. Stool and peripheral blood (PB) samples will be
collected at time of consent for therapy. TNBC patients will be treated with the standard
of care neoadjuvant chemotherapy. At mid-treatment (MT), an elective tumor biopsy will be
performed and stool and PB samples will be collected. At time of surgery, after the
completion of neoadjuvant chemotherapy (at the discretion of the medical oncologist),
resected tumor and "normal" adjacent non-tumor tissue, stool and PB samples will be
collected.
Pre- , mid- and post-therapy immune phenotyping/profiling will be determined in PB
samples and patient biopsies. The overall composition of the gut microbiome will also be
determined in patient stool samples.
The overview of the study is presented below:
1. Regimen and duration of neoadjuvant chemotherapy is at the discretion of the medical
oncologist.
2. Cycle 1 refers to first dose of each treatment.
3. Tumor morphology, IHC and FISH will be performed at diagnosis of TNBC. Criteria for
newly diagnosed TNBC: <1% of ER and PR immunoreactivity and HER2- by FISH or IHC
staining 0 or 1+ and T1 (T1: <1.5 cm) mass lesion or greater.
4. For correlative studies, collection of PB will be at day 1 of cycle 1, day 1 of
cycle 1 of T and end of treatment, prior to surgery. Eight 8x tubes, seven (7)
yellow top tubes (BD Vacutainer ACD Solution A Blood Collection tubes - 8.5ml) and
one (1) Streck tube . Immunophenotying, gene expression profiling and assessment of
cytokine/chemokine and other mediators production will be performed.
5. For correlative studies, Stool collection will be collected up to 48 hours prior to
drug administration on day 1 of cycle 1 and day of surgery. Sequencing of the gut
and intratumoral microbiome and gene-associated pathways will be performed by 16S
rRNA and shotgun metagenomics sequencing.
6. For correlative studies, immunostaining of fixed tissue for PD-L1 or other immune
marker expression on tumor cells and for the in situ presence of various T cell
subset markers with PD1 expression will be performed. Isolation of DNA and RNA will
be performed from formalin-fixed tissues.
7. Tumor biopsy for mid-treatment (MT). This biopsy will be offered and performed upon
consent of patient.
8. This tissue will be provided by Pathology Department upon processing of surgical
specimen.
