Transcription factor-nucleosome dynamics from plasma cfDNA identifies ER-driven states in breast cancer

Genome-wide binding profiles of estrogen receptor (ER) and FOXA1 reflect cancer state in ER+ breast cancer. However, routine profiling of tumor transcription factor (TF) binding is impractical in the clinic. Here, we show that plasma cell-free DNA (cfDNA) contains high-resolution ER and FOXA1 tumor binding profiles for breast cancer. Enrichment of TF footprints in plasma reflects the binding strength of the TF in originating tissue. We defined pure in vivo tumor TF signatures in plasma using ER+ breast cancer xenografts, which can distinguish xenografts with distinct ER states. Furthermore, state-specific ER-binding signatures can partition human breast tumors into groups with significantly different ER expression and mortality. Last, TF footprints in human plasma samples can identify the presence of ER+ breast cancer. Thus, plasma TF footprints enable minimally invasive mapping of the regulatory landscape of breast cancer in humans and open vast possibilities for clinical applications across multiple tumor types.

Abstract 2611: Transcription factor-nucleosome dynamics inferred from plasma cfDNA delineates tumor and tumor-microenvironment phenotype

Our current understanding of solid tumors and their progression primarily relies on in vitro models, cell lines, patient-derived xenografts, and scarce data from invasive tissue biopsies from patients. The ability to monitor changes in chromatin structure and transcription factor binding in tumor cells using a minimally invasive approach in humans has the potential to revolutionize our understanding of disease progression and treatment resistance. In this study, we use the example of estrogen receptor (ER) positive breast cancer, the most common disease subtype, and define the ER axis from plasma cell-free DNA (cfDNA). While lymphoid/myeloid cell turnover represents the dominant source of cfDNA in the bloodstream, a detectable fraction of DNA from tumor tissue-of-origin can be found in patients with solid cancers. cfDNA is the product of the action of endogenous nucleases on chromatin; and retains the map of epigenomes from cells of origin. Our method therefore non-invasively captures TF-nucleosome dynamics in tumor tissue-of-origin using plasma cfDNA. First, we show that we can reliably identify the active binding of hematopoietic pioneer factor PU.1 and CTCF from cfDNA of healthy humans and cancer patients. Then to define cfDNA binding of disease specific TF ER, we used ER+ patient-derived xenograft (PDX) models allowing for a clear separation of tumor signal from hematopoietic background. This allowed us to establish the sensitivity and specificity of our approach. We also identified the subset of CUT&RUN-defined ER binding sites that feature the strongest binding in vivo from both lymphocyte background as well as cancer cells. Furthermore, we can define the active binding sites of pioneer factor FOXA1, which facilitates ER binding by opening the chromatin. Based on the TF protection levels from cfDNA we were able to define tumor as well as hematopoietic-specific TF binding sites that can serve as potential hotspots to monitor ER+ disease state at around 1% tumor fraction. These data demonstrate our ability to simultaneously monitor TF and nucleosome dynamics at disease sites just from plasma that can enable real-time monitoring of disease phenotype in a minimally invasive manner.

Citation Format: Satyanarayan Rao, Amy Han, Alexis Zukowski, Etana Kopin, Peter Kabos, Srinivas Ramachandran. Transcription factor-nucleosome dynamics inferred from plasma cfDNA delineates tumor and tumor-microenvironment phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2611.

Fibroblast subtypes define a metastatic matrisome in breast cancer

Small primary breast cancers can show surprisingly high potential for metastasis. Clinical decision-making for tumor aggressiveness, including molecular profiling, relies primarily on analysis of the cancer cells. Here we show that this analysis is insufficient - that the stromal microenvironment of the primary tumor plays a key role in tumor cell dissemination and implantation at distant sites. We previously described 2 cancer-associated fibroblasts (CAFs) that either express (CD146+) or lack (CD146-) CD146 (official symbol MCAM, alias MUC18). We now find that when mixed with human breast cancer cells, each fibroblast subtype determines the fate of cancer cells: CD146- fibroblasts promoted increased metastasis compared with CD146+ fibroblasts. Potentially novel quantitative and qualitative proteomic analyses showed that CD146+ CAFs produced an environment rich in basement membrane proteins, while CD146- CAFs exhibited increases in fibronectin 1, lysyl oxidase, and tenascin C, all overexpressed in aggressive disease. We also show clinically that CD146- CAFs predicted for likelihood of lymph node involvement even in small primary tumors (<5 cm). Clearly small tumors enriched for CD146- CAFs require aggressive treatments.

Abstract PD9-09: Proteomic analysis of extracellular matrix helps define drivers of metastatic progression

Tumor microenvironment (TME) plays a central role in the development of distant metastasis. However, given its complexity, successful targeting of TME will require a detailed understanding of its composition. Cancer-associated fibroblasts represent a large component of TME and are a major contributor to the extracellular matrix (ECM). Previously, we demonstrated the presence of two fibroblast sub-populations (CDCP1pos vs CD146pos fibroblasts) in breast cancer TME, which determine therapeutic response in estrogen receptor (ER) positive breast cancer. We hypothesized that the same fibroblast subtypes would also influence ECM composition and alter the metastatic potential of breast cancer cells. Here, we present the development of a novel fibroblast driven orthotopic model of ER+ breast cancer metastasis, which we combined with an innovative proteomics approach to precisely quantify extracellular matrix proteins.

Results: 1.CDCP1pos fibroblasts promote increased breast cancer cell mobility, invasion and metastasis compared to CD146pos fibroblasts.We demonstrate that CDCP1pos fibroblasts significantly increase the invasion potential of breast cancer cells, when compared to CD146pos fibroblasts. Orthotopic co-implantation of ER+ tumor cells with CDCP1pos fibroblasts into the mammary fat pad of mice more frequently drives distant organ metastases to lung and brain when compared with tumors implanted with CD146pos fibroblasts. 2. Proteomic analysis of ER+ tumors influenced by CDCP1pos fibroblasts revealed known and novel drivers of breast cancer metastasis. Breast cancer cells mixed with CDCP1pos fibroblasts produce a non-uniform collagen orientation to the tumor boarder. Our novel proteomic analysis of TME specific proteins revealed that tumors influenced by CDCP1pos fibroblasts have high expression of many ECM proteins linked to increased risk of breast cancer metastasis, including TNC, FN1, COL5A3, and FBN1 among others. Derived proteomic TME signature accurately predicted lymph node involvement in patients who presented with early stage (T0 and T1) tumors in a cohort of 1,009 breast cancer patients from Cancer Genome Atlas Database. 3. Inhibiting fibroblast production of Tenascin C (TNC) results in decreased breast cancer cell invasion. Our in vitro mixed co-culture models, which contain ER+ breast cancer cells with both fibroblast subtypes, demonstrate that only CDCP1pos fibroblasts produce TNC. Furthermore, in spheroid assays with CDCP1posfibroblasts and breast cancer tumor cells, invasion is inhibited by TNC knockdown. The invasion phenotype can be rescued by addition of EGF, which suggests TNC promotes invasion via EGFR signaling.

Conclusion: Metastatic spread of cancer cells relies heavily on TME alterations and makeup of the extracellular matrix. Our data suggest that fibroblast composition directly influences ECM properties and metastatic potential in breast cancer. Taken together, we believe that a better understanding of ECM composition will lead to a more personalized approach to breast cancer treatment.

Citation Format: Brechbuhl HM, Barrett AS, Kopin E, Gillen A, Hagen J, Johnson L, Finaly-Shultz J, Sartorius CA, Hansen KC, Kabos P. Proteomic analysis of extracellular matrix helps define drivers of metastatic progression [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD9-09.

Optimizing the transduction efficiency of capsid-modified AAV6 serotype vectors in primary human hematopoietic stem cells in vitro and in a xenograft mouse model in vivo

BACKGROUND AIMS

Although recombinant adeno-associated virus serotype 2 (AAV2) vectors have gained attention because of their safety and efficacy in numerous phase I/II clinical trials, their transduction efficiency in hematopoietic stem cells (HSCs) has been reported to be low. Only a few additional AAV serotype vectors have been evaluated, and comparative analyses of their transduction efficiency in HSCs from different species have not been performed.

METHODS

We evaluated the transduction efficiency of all available AAV serotype vectors (AAV1 through AAV10) in primary mouse, cynomolgus monkey and human HSCs. The transduction efficiency of the optimized AAV vectors was also evaluated in human HSCs in a murine xenograft model in vivo.

RESULTS

We observed that although there are only six amino acid differences between AAV1 and AAV6, AAV1, but not AAV6, transduced mouse HSCs well, whereas AAV6, but not AAV1, transduced human HSCs well. None of the 10 serotypes transduced cynomolgus monkey HSCs in vitro. We also evaluated the transduction efficiency of AAV6 vectors containing mutations in surface-exposed tyrosine residues. We observed that tyrosine (Y) to phenylalanine (F) point mutations in residues 445, 705 and 731 led to a significant increase in transgene expression in human HSCs in vitro and in a mouse xenograft model in vivo.

CONCLUSIONS

These studies suggest that the tyrosine-mutant AAV6 serotype vectors are the most promising vectors for transducing human HSCs and that it is possible to increase further the transduction efficiency of these vectors for their potential use in HSC-based gene therapy in humans.

An intravaginal ring for the simultaneous delivery of multiple drugs

Intravaginal delivery of microbicide combinations is a promising approach for the prevention of sexually transmitted infections, but requires a method of providing simultaneous, independent release of multiple agents into the vaginal compartment. A novel intravaginal ring (IVR) platform has been developed for simultaneous delivery of the reverse-transcriptase inhibitor tenofovir (TFV) and the guanosine analogue antiviral acyclovir (ACV) with independent control of release rate for each drug. The IVR is based on a pod design, with up to 10 individual polymer-coated drug cores embedded in the ring releasing through preformed delivery channels. The release rate from each pod is controlled independently of the others by the drug properties, polymer coating, and size and number of delivery channels. Pseudo-zero-order in vitro release of TFV (144 ± 10 µg day) and ACV (120 ± 19 µg day⁻¹) from an IVR containing both drugs was sustained for 28 days. The mechanical properties of the pod IVR were evaluated and compared with the commercially available Estring® (Pfizer, NY, NY). The pod-IVR design enables the vaginal delivery of multiple microbicides with differing physicochemical properties, and is an attractive approach for the sustained intravaginal delivery of relatively hydrophilic drugs that are difficult to deliver using conventional matrix IVR technology.

Microbial biofilms on the surface of intravaginal rings worn in non-human primates

Millions of intravaginal rings (IVRs) are used by women worldwide for contraception and for the treatment of vaginal atrophy. These devices also are suitable for local and systemic sustained release drug delivery, notably for antiviral agents in human immunodeficiency virus pre-exposure prophylaxis. Despite the widespread use of IVRs, no studies have examined whether surface-attached bacterial biofilms develop in vivo, an important consideration when determining the safety of these devices. The present study used scanning electron microscopy, fluorescence in situ hybridization and confocal laser scanning microscopy to study biofilms that formed on the surface of IVRs worn for 28 days by six female pig-tailed macaques, an excellent model organism for the human vaginal microbiome. Four of the IVRs released the nucleotide analogue reverse transcriptase inhibitor tenofovir at a controlled rate and the remaining two were unmedicated. Large areas of the ring surfaces were covered with monolayers of epithelial cells. Two bacterial biofilm phenotypes were found to develop on these monolayers and both had a broad diversity of bacterial cells closely associated with the extracellular material. Phenotype I, the more common of the two, consisted of tightly packed bacterial mats approximately 5 µm in thickness. Phenotype II was much thicker, typically 40 µm, and had an open architecture containing interwoven networks of uniform fibres. There was no significant difference in biofilm thickness and appearance between medicated and unmedicated IVRs. These preliminary results suggest that bacterial biofilms could be common on intravaginal devices worn for extended periods of time.

Use of ultrasonography in the difficult postmenopausal dilation and curettage

Six patients from our series of 21 cases are presented to illustrate the use of real-time ultrasound to complete the D&C. Thirteen of the 21 had concomitant ultrasound because of stenosis of the cervix or vagina, three because of previous vaginal procedures that distorted the anatomy, and five because of concern regarding perforation.