Benjamin Ziman, Ph.D. Email & Phone Number

Los Angeles, California, United States

As a postdoctoral research fellow at USC, I am investigating upper aerodigestive (Esophageal and Head & Neck squamous cell carcinoma) malignancies under the mentorship of Dr. Dechen Lin. Using genetically engineered stable over-expression and knockdown cancer cells I am investigating how transcription factors can push cells to become more metastatic. I am performing in vivo studies to analyze metastasis and further validating tumors with H&E staining. I am also performing orthotopic injects in vivo to analyze tumor immune infiltration and administering immune check point blockade mAbs to elicit an immune response to reduce tumor growth. Additionally, I am using FDA approved drugs to repress cell growth and reduce metastatic potential. Lastly, using the FDA approved drugs, I am seeking mechanisms of action for regulating gene expression. During this time, I am mentoring an undergraduate student researcher. I am teaching this student various molecular biology techniques and guiding him through various protocols. His contributions will lead to a co-author position on an upcoming publication. Additionally, I have created several new SOPs and helped make modifications to our IACUC protocol. I continue to work directly with EH&S to ensure that safety practices are being followed and guide safety officers through our inspections. I am actively participating in department seminars, department journal clubs, lab meetings, and lab journal clubs.

Los Angeles Metropolitan Area

Under the co-mentorship of Dr. Dechen Lin and Dr. Uttam Sinha, I began investigating upper aerodigestive (Esophageal and Head & Neck squamous cell carcinoma) malignancies. Using single cell RNA-seq data analysis from both cancer cell lines and cancer patient samples, with the help of bioinformaticians, we were able to identify cancer specific transcription factors that have high metastatic potential. Furthermore, we were able to create our own 14 gene metastatic signature. I created genetically engineered stable knockdown and over-expression cell lines using viral vectors. Metastatic potential was validated transcriptionally with qPCR using our metastatic gene signature as well with in vitro cell migration and wound healing assays. Further validation was done in vivo, using tail vein injections in mice with genetically engineered cancer cells to observe metastasis of target organs.In addition to this new project, I published my previous work as a first author in the Nature publishing group (DOI: 10.1038/s41419-024-06488-x). Additionally, I helped to establish a biobank comprised of tissue and blood samples from patients that underwent surgery who suffered from Head & Neck Cancer. I processed tissue samples and isolated PBMCs from blood samples. I also accessed patients charts and created a spreadsheet with patient’s information corresponding to the samples being collected. During this time, I helped mentor two high school students, teaching them various molecular biology techniques. I also mentored a 3rd year medical student and rotating graduate student, guiding them through various protocols, leading to their contribution on publications. I created SOPs and helped modify IACUC protocols. I worked directly with EH&S to ensure that safety practices were being followed and guided them through safety inspections. I also participated in department seminars, department journal clubs, lab meetings, and lab journal clubs.

Los Angeles, California, United States

I continued working under the mentorship of Dr. Dechen Lin at USC. I furthered my project investigating the role of FOXM1 in EAC. Using publicly available and in house sequencing data, I identified upstream signaling regulation of FOXM1 and was able to validate these results with small molecule inhibitors, by performing ChIP-PCR, western blotting, and qPCR. I explored the novel role of FOXM1 regulating the immune system by performing in vivo tumor growth assays in immune competent mice, disassociating tumors, and running flow cytometry of a panel of immune cell populations. Using mice, I isolated primary immune CD8+ T cells and performed migration and cytotoxic co-culture experiments. I also used ELISA assays to determine chemokines released by cancer cells that are required for CD8+ T cell chemotaxis and used neutralizing monoclonal antibodies to validate mechanisms of CD8+ T cell recruitment. I helped contribute as a co-first author on literature review of genomic and epigenomic characterization of tumor organoid models (DOI:10.3390/cancers14174090). Additionally, I collaborated with others and performed experiments, and leading to co-authorship on publications (DOI: 10.1126/SCITRANSLMED.ABQ6146, DOI: 10.1186/s13059-023-03035-3).Additionally, I was responsible for setting up the new lab at USC. This included packing and unpacking all materials and equipment, completing paperwork for the lab to be operational. I created SOPs and helped with making IACUC protocols. I was responsible for doing inventory and organizing our cell line bank. I acted as the lab manager, ensuring that orders were placed, quotes and PO#s were obtained, and the animal husbandry in the vivarium was maintained. I worked directly with EH&S to ensure that safety practices were being followed and guided them through safety inspections. I also participated in department seminars, department journal clubs, lab meetings, and lab journal clubs.

Los Angeles Metropolitan Area

Working under the mentorship of Dr. Dechen Lin, I investigated the role of transcription factors driving cancer progression in Esophageal Adenocarcinoma (EAC). Using large scale methylation data (Whole Genome Bisulfite Sequencing) from EAC cancer patient tissue samples, with the help of our labs bioinformaticians, we identified EAC cancer specific transcription factors. In vitro, I created genetically engineered stable knockdown (shRNA) and knockout (CRISPR Cas9) cells by infecting cell lines with viral vectors. By performing ChIP and RNA interference, we did RNA-seq and ChIP-seq to reveal transcriptional regulation, determine impacted signaling pathways, and identify direct binding targets. This allowed us to produce a gene signature to evaluate the activity of FOXM1. Using small molecule inhibitors, I evaluated cytotoxicity and regulation of FOXM1 activity. Additionally, I performed cellular proliferation assays and in vivo tumor growth experiments in the mouse model.In addition to my own independent project, I collaborate with others (DOI:10.3390/cancers15225377). I created new SOPs and helped with making modifications to IACUC protocols. I took on a role as the lab manager, ensuring that orders were placed in a timely manner, contacting companies to produce PO#’s, and requesting for quotes. I was responsible for lab safety, working with EH&S to ensure that the lab was running under the safety standards of the research institution. I participated in weekly lab meetings and journal clubs presenting my research findings and peer-reviewed literature articles respectively.

Merced, California, United States

Working for the School of Natural Sciences at the University of California Merced, I instructed the Molecular Cell Biology lab for undergraduate students. I helped make modifications to the syllabus, bringing forth new ideas, and update SOPs for various protocols. I helped with grading assignments and producing assigned final grades.

Merced, California Area

Under the mentorship of Dr. Nestor Oviedo, I took part in several independent and collaborative research projects. I investigated stem cell fate in vivo and how it influences regeneration upon genetic alteration (DOI: 10.1016/j.isci.2020.101665). I uncovered how metabolic regulators can influence organismal growth, feeding behavior patterns, and differentiation of stem cell populations (DOI:10.1242/jcs.239467). I also participated on a wide range of projects from how the nervous system influences cancer, to how DNA damage repair mechanisms influence regeneration, host pathogen interaction (DOI: 10.3389/fmicb.2020.629526), and how bioelectricity can influence cell migration and stem cell fate (DOI: 10.1242/jcs.259304, DOI: 10.1089/bioe.2020.0026). Genetic manipulations were performed using microinjections in vivo. I established novel techniques for exploring feeding behaviors. Used several techniques to visualize how stem cells differentiate into different organs, including fluorescent in situ hybridization and immunohistochemistry. Measured protein and gene expression using western blotting and qPCR respectively. I created new SOPs including a peer-reviewed protocol in the Cell Press Journal, STAR Protocols (DOI: 10.1016/j.xpro.2020.100274). Additionally, I took on a managerial role, ensuring that reagents were well stocked and that our lab was working within the university’s safety standards. During this time, I mentored several undergraduate research projects, leading to their contributions on publications. I also presented results and peer-reviewed literature articles in weekly meetings.

Merced, California Area

During my time as a graduate student teaching assistant, I instructed numerous undergraduate biology courses (Biological Math Modeling and Statistics, Embryos and Development Lab, Genetics, Introductory Biology, Molecular Cell Biology, Molecular Cell Biology Lab). I worked directly with faculty members to help develop a syllabus and course materials. I taught students in weekly discussion and occasional lectures. I instructed students through several protocols during instructional labs. I also was responsible for grading assignments and administrations of final grades.

Merced, California Area

Under the mentorship of Dr. Fred Wolf, I investigated how alcohol can alter protein histone deacetylation in the brain of Drosophila. During this process, I helped establish a gene knockout model through genetic breeding. Upon alcohol exposure, I dissected brains and performed immunohistochemistry, which was visualized using a confocal microscope. I also master several molecular cell biology techniques such as PCR and Western blotting. Additionally, I presented my results and peer-reviewed publications in weekly lab meetings.

Doctor Of Philosophy (Phd), Quantitative Systems Biology

Thesis: Determining how metabolic proteins can influence feeding behavior, organismal growth, and stem cell fate in the adult body.

Bachelor Of Science (Bs), Molecular Biology