In this issue:



• Announcements
• Upcoming Seminars
• 11/11/25: From Complexity to Clarity: Characterizing Biologics with Emerging Mass Spectrometry Tools
• 11/12/25: At the Core of Cardiac Function: Surgical and Echocardiographic Approaches in Rodent Cardiovascular Phenotyping
• Animal Models Core Group Forming
• Animal Research Vaporization Calibration Service
• Updated Core Facility Presentations

• Core Facilities Spotlight
• Cell and Animal Radiation Core
• Clinical Research Collaboration Unit – REDCap Development Group
• Live Cell Imaging Core: Penn Dental
• OCRC Tumor BioTrust
• Penn Genomics & Sequencing Core

Announcements: 11/11/25 - From Complexity to Clarity: Characterizing Biologics with Emerging Mass Spectrometry Tools

From Complexity to Clarity: Characterizing Biologics with Emerging Mass Spectrometry Tools

Tuesday, November 11th, 2025

1:30 - 5:30 PM | Campus of the University of Pennsylvania

John Morgan Building Reunion Hall

Invited Speakers include:

Rebecca D'Esposito | Waters 

Ben Draper | Megadalton Solutions

Hannah Geisler | University of Pennsylvania (Mitchell Lab)

Siavash Vahidi | University of Guelph

Free to the Public | Space-Limited | RSVP Required

RSVP at: https://docs.google.com/forms/d/e/1FAIpQLSfOuHGzyYhF1NgMoXy8RXNw5VwGaWcdXYuhxcn7rap_ohL5SA/viewform?pli=1

Sponsored by:

The Department of Biochemistry and Biophysics, Perelman School of Medicine

Johnson Foundation Biophysical & Structural Biology Core Facilities,

with kind support from Waters Corporation

Announcements: 11/12/25 - At the Core of Cardiac Function: Surgical and Echocardiographic Approaches in Rodent Cardiovascular Phenotyping

At the Core of Cardiac Function: Surgical and Echocardiographic Approaches in Rodent Cardiovascular Phenotyping

Wednesday, November 12th, 2025

12pm

Smilow 11-146

Presented by: The Rodent Cardiovascular Phenotyping Core

For more information please visit: https://www.med.upenn.edu/cvi/

Announcements: Animal Models Core Group Forming

A group of cores that use animal models is forming. The group’s primary goal is to mutually assist one another with matters specifically related to the use of animals in core settings. The group will promote core facilities as an effective means to reduce and refine the number of animals required to attain robust results.

The core-directors-driven group will share SOPs related to governing bodies such as ULAR, IACUC, and EHRS. The exchange of approaches utilized to address regulatory matters in one core, may help other cores operate more efficiently.

The Animal Model Cores group will foster collaboration between cores seeking to facilitate core-to-core projects. Within-animal findings between specialized cores would add breadth to, and strengthen, our users’ projects. Such cross-discipline projects will be explored and the logistics of animal relocations will be deliberated with the help of ULAR.

Business and routine matters related to animal research cores will be discussed. In the future the group will seek advice from other cores regarding ex vivo sample preparation (for histology, molecular, other), data management, finances, as well as other matters that may arise. Also, the group will search for means to highlight the expertise and capabilities of UPenn core facilities.

Informal round table meetings of the Animal Model Cores group will occur quarterly with the next meeting planned for early January 2026. For more information, please contact Tim O’Brien at obrienw@pennmedicine.upenn.edu or April Weakley at aweakley@pennmedicine.upenn.edu. 

Announcements: Animal Research Vaporization Calibration Service

The fee for this service is $200 per vaporizer, payable only by funds transfer.

Vaporizer calibration will be completed within a week of receipt:

• Bring vaporizer to 302 John Morgan Building (use the Johnson Pavilion elevators)
• M-F, 10am – 4pm
• Label vaporizer with PI's name, email, phone number (masking tape is OK)
• Bring the completed funds transfer form
• Bring vaporizer partially (< 1/2) filled with correct liquid anesthetic agent
• Keep vaporizer upright during transport

Following the Association for the Assessment and Accreditation of Laboratory Animal Care (AAALAC) recommendations and IACUC guidelines, the maximum allowable time between vaporizer calibration services is two years.

Contact Weiming Bu: weiming.bu@pennmedicine.upenn.edu 

Announcements: Updated Core Facility Video Presentations

Thank you to everyone who presented at Cores Day 2025! The video presentations have now been uploaded to the Biomedical Research Core Facility Presentations page. Please click here to view them.

Core Facilities Spotlight: Cell and Animal Radiation Core - RRID:SCR_022377

We are excited to announce that we are taking the Small Animal Radiation Research Platform (SARRP) education to a global level through a landmark partnership with Penn Medicine's OncoLink and our Small Animal Irradiator Vendor Xstral.

This extensive SARRP Education Series provides the global research community with world-class resources in Image-Guided Radiation Therapy (IGRT) with on-demand training modules and opportunities for in-person training sessions.

The core also participated in the international symposium on FLASH Radiotherapy held by the Department of Radiation Oncology at Penn, in March 2025.

Representative Publications:

Ni H, Reitman ZJ, Zou W, et al. FLASH radiation reprograms lipid metabolism and macrophage immunity and sensitizes medulloblastoma to CAR-T cell therapy. Nat Cancer. 2025;6(3):460-473. https://doi.org/10.1038/s43018-025-00905-6

Cramer, E., Dobiasch, S., & Liu, X., Combs, S. E, et al. Full-body deep learning-based automated contouring of contrast-enhanced murine organs for small animal irradiator CBCT. 2024 Feb 4. https://doi.org/10.48550/arXiv.2402.02469

Kim K, Kim MM, Skoufos G, et al. FLASH Proton Radiation Therapy Mitigates Inflammatory and Fibrotic Pathways and Preserves Cardiac Function in a Preclinical Mouse Model of Radiation-Induced Heart Disease. Int J Radiat Oncol Biol Phys. 2024;119(4):1234-1247. https://doi.org/10.1016/j.ijrobp.2024.01.224

Lim TL, Morral C, Verginadis II, et al. Early Inflammation and Interferon Signaling Direct Enhanced Intestinal Crypt Regeneration after Proton FLASH Radiotherapy. Preprint. bioRxiv. 2024;2024.08.16.608284. Published 2024 Aug 19. https://doi.org/10.1101/2024.08.16.608284

L. Loza, K. Ruppert, J. Chen, H. Hamedani, M.K. Ismail, F. Amzajerdian, I. Duncan, S. Kadlecek, and R.R. Rizi. Assessing Radiation-induced Lung Injury Using a Chemical Shift Imaging-based CSSR Technique [abstract]. Am J Respir Crit Care Med 2024;209:A4494. https://doi.org/10.1164/ajrccm-conference.2024.209.1_MeetingAbstracts.A4494

Morral C, Ayyaz A, Kuo HC, et al. p53 promotes revival stem cells in the regenerating intestine after severe radiation injury. Nat Commun. 2024;15(1):3018. Published 2024 Apr 8. https://doi.org/10.1038/s41467-024-47124-8

Orlovskiy S, Gupta PK, Roman J, et al. Lonidamine Induced Selective Acidification and De-Energization of Prostate Cancer Xenografts: Enhanced Tumor Response to Radiation Therapy. Cancers (Basel). 2024;16(7):1384. Published 2024 Mar 31. https://doi.org/10.3390/cancers16071384

Verginadis II, Velalopoulou A, Kim MM, et al. FLASH proton reirradiation, with or without hypofractionation, mitigates chronic toxicity in the normal murine intestine, skin, and bone. Preprint. bioRxiv. 2024;2024.07.08.602528. Published 2024 Jul 11. https://doi.org/10.1101/2024.07.08.602528

Amit U, Uslu U, Verginadis II, et al. Proton radiation boosts the efficacy of mesothelin-targeting chimeric antigen receptor T cell therapy in pancreatic cancer. Proc Natl Acad Sci U S A. 2024;121(31):e2403002121. https://doi.org/10.1073/pnas.2403002121

Kostopoulos N, Costabile F, Krimitza E, et al. Local radiation enhances systemic CAR T-cell efficacy by augmenting antigen crosspresentation and T-cell infiltration. Blood Adv. 2024;8(24):6308-6320. https://doi.org/10.1182/bloodadvances.2024012599

Core Facilities Spotlight: Clinical Research Collaboration Unit - RRID:SCR_022404

What’s new at the Clinical Research Collaboration Unit (CRCU)?

Are you a researcher in need of a REDCap project to support your research, but don’t have the time or technical support to develop your project? Whether you're under tight deadlines, limited by technical capacity, or managing a complex study, we’re here to help.

We are excited to announce the launch of the new REDCap Development Group, offering REDCap support to all investigators and research teams at the University of Pennsylvania on a fee-for-service basis. The REDCap Development Group, within the Clinical Research Collaboration Unit (CRCU), partners with researchers to provide expert, on-demand REDCap project development and support. From building basic surveys to advanced workflows with automation, eConsent, and text messaging — we handle the REDCap development so you can focus on your science.

Why Choose Us?

• Save Time – Get your project built right the first time
• Access Expertise – Leverage REDCap best practices and advanced features
• Ensure Compliance – Align with HIPAA, IRB, and institutional standards
• Flexible Support – From quick fixes to full project builds

For more information, see https://www.cceb.med.upenn.edu/redcapdev

Core Facilities Spotlight: Live Cell Imaging Core (Penn Dental) - RRID:SCR_022443 

We are happy to announce that the PDM Confocal Imaging Core has upgraded its analysis software offering enhanced capabilities including AI powered analyses and automated object tracking to better support your research needs. The software can also be utilized independently of the core’s microscope, providing greater flexibility for your work. The key upgrades include:

1. NIS-Elements 6.10.01 Advanced Research software
2. NIS-Elements General Analysis 3 (GA3) module (3D): to create workflows that include pre-processing, thresholding, segmentation, data analysis, and graphical outputs
3. NIS.ai: to allow AI powered analysis (Convert.ai, Denoise.ai, Enhance.ai, Segment.ai and SegmentObject.ai)
4. Tracking module: enables automated object tracking with advanced tracking options in 2D and 3D time lapse images, supporting complex motion dynamics analysis

Core Facilities Spotlight: OCRC Tumor BioTrust Collection - RRID:SCR_022387

The Ovarian Cancer Research Center Tumor BioTrust Collection collects fresh cancer tissue specimens, as well as plasma, serum, peripheral blood mononuclear cells (PBMC), blood and other biological samples from various cancer cases with a focus on gynecologic cancers. We also house formalin fixed paraffin embedded (FFPE) samples including tissue microarray (TMA) construction and immunohistochemistry. Samples collected through the Penn Legacy Tissue Program (PLTP) (e.g., rapid autopsy) are also available and a quote can be provided upon request.

We would love to work with investigators to prospectively collect specific samples to support their research within the Penn research community as well as outside academic institutions. We will be working with biotech/bio-pharma companies if it is within the confines of a collaboration.

We are offering the following sample types:

• Fresh Tumor Tissue
• Fresh Ascites Fluid
• Frozen Tumor Tissue
• Enzyme Digested Tumor Cells
• Serum & Plasma
• Peripheral Blood Mononuclear Cells (PBMC)
• OCT
• Formalin Fixed Paraffin Embedded (FFPE)
• Tissue Microarray (TMA)
• Samples from rapid autopsies through our Penn Legacy Tissue Program (PLTP)

More info about the core and pricing can be found at: https://www.med.upenn.edu/OCRCBioTrust/

Representative Publications:

LINE-1 ORF1p expression occurs in clear cell ovarian carcinoma precursors and is a candidate blood biomarker

Pamela R de Santiago, Sho Sato, Stephanie J Zhang, Meaghan C Dougher, Kyle M Devins, Agnes J Bilecz, Sagar Rayamajhi, Gabriel Mingo, Hannah S Rendulich, Yi Feng, Connie Wu, Martin S Taylor, Yelena Zhuravlev, Euihye Jung, Dalia K Omran, Tian-Li Wang, Ie-Ming Shih, Lauren E Schwartz, Sarah Kim, Mark A Morgan, Janos L Tanyi, Kathleen H Burns, Ernst Lengyel, Carlos Parra-Herran, Andrew K Godwin, David R Walt, Ronny Drapkin

PMID: 40050409 PMCID: PMC11885553 DOI: 10.1038/s41698-025-00849-1

Early Detection of Ovarian Cancer Using Cell-Free DNA Fragmentomes and Protein Biomarkers

Jamie E Medina, Akshaya V Annapragada, Pien Lof , Sarah Short, Adrianna L Bartolomucci, Dimitrios Mathios, Shashikant Koul, Noushin Niknafs, Michaël Noë, Zachariah H Foda, Daniel C Bruhm, Carolyn Hruban, Nicholas A Vulpescu, Euihye Jung, Renu Dua, Jenna V Canzoniero, Stephen Cristiano, Vilmos Adleff, Heather Symecko, Daan van den Broek, Lori J Sokoll, Stephen B Baylin, Michael F Press, Dennis J Slamon, Gottfried E Konecny, Christina Therkildsen, Beatriz Carvalho, Gerrit A Meijer, Claus Lindbjerg Andersen, Susan M Domchek, Ronny Drapkin, Robert B Scharpf, Jillian Phallen, Christine A R Lok, Victor E Velculescu 

PMID: 39345137 PMCID: PMC11726017 DOI: 10.1158/2159-8290.CD-24-0393

Early Detection of Ovarian Cancer Using Cell-Free DNA Fragmentomes and Protein Biomarkers - PMC

CHK1 inhibitor SRA737 is active in PARP inhibitor resistant and CCNE1 amplified ovarian cancer

Haineng Xu, Sarah B Gitto, Gwo-Yaw Ho, Sergey Medvedev, Kristy Shield-Artin, Hyoung Kim, Sally Beard, Yasuto Kinose, Xiaolei Wang, Holly E Barker, Gayanie Ratnayake, Wei-Ting Hwang; Australian Ovarian Cancer Study; Ryan J Hansen, Bryan Strouse, Snezana Milutinovic, Christian Hassig, Matthew J Wakefield, Cassandra J Vandenberg, Clare L Scott, Fiona Simpkins 

CD137+ tumor infiltrating lymphocytes predicts ovarian cancer survival.

Elizabeth A Tubridy, Monika A Eiva, Fang Liu, Dalia K Omran, Stefan Gysler, Erica G Brown, Allison G Roy, Yuyan Zeng, Jinhee Oh, Quy Cao, Sarah B Gitto, Daniel J Powell Jr PMID: 38290413 DOI: 10.1016/j.ygyno.2024.01.029

CHK1 inhibitor SRA737 is active in PARP inhibitor resistant and CCNE1 amplified ovarian cancer.

Haineng Xu, Sarah B Gitto, Gwo-Yaw Ho, Sergey Medvedev, Kristy Shield-Artin, Hyoung Kim, Sally Beard, Yasuto Kinose, Xiaolei Wang, Holly E Barker, Gayanie Ratnayake, Wei-Ting Hwang, Australian Ovarian Cancer Study; Ryan J Hansen, Bryan Strouse, Snezana Milutinovic, Christian Hassig, Matthew J Wakefield, Cassandra J Vandenberg, Clare L Scott, Fiona Simpkins. PMID: 39021796 PMCID: PMC11253285 DOI: 10.1016/j.isci.2024.109978

Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors.

Hippen, A.A., Omran, D.K., Weber, L.M. et al. Performance of computational algorithms to deconvolve heterogeneous bulk ovarian tumor tissue depends on experimental factors. Genome Biol 24, 239 (2023). https://doi.org/10.1186/s13059-023-03077-7

Functional neuronal circuits promote disease progression in cancer.

Restaino AC, Walz A, Vermeer SJ, Barr J, Kovács A, Fettig RR, Vermeer DW, Reavis H, Williamson CS, Lucido CT, Eichwald T, Omran DK, Jung E, Schwartz LE, Bell M, Muirhead DM, Hooper JE, Spanos WC, Drapkin R, Talbot S, Vermeer PD.

Science Advances 2023 May 10;9(19):eade4443. doi: 10.1126/sciadv.ade4443.

Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker.

Taylor MS, Connie W, Fridy PC, Zhang SJ, Senussi Y, Wolters JC, Cheng WC, Heaps J, Miller BD, Mori K, Cohen L, Jiang H, Molloy KR, Norden BL, Chait BT, Goggins M, Bhan I, Franses JW, Yang X, Taplin ME, Wang X, Christiani DC, Johnson BE, Meyerson M, Uppaluri R, Egloff AM, Denault EN, Spring LM, Wang TL, Shih IM, Jung E, Arora KS, Zukerberg LR, Yilmaz OH, Chi G, Matulonis UA, Song Y, Nieman L, Parikh AR, Strickland M, Corcoran RB, Mustelin T, Eng G, Yilmaz ÃH, Skates SJ, Rueda BR, Drapkin R, Klempner SJ, Deshpande V, Ting DT, Rout MP, LaCava J, Walt DR, Burns KH.

BioRxiv 2023 Mar 17:2023.01.25.525462. doi: 10.1101/2023.01.25.525462. Preprint

Folate Receptor Beta as a Direct and Indirect Target for Antibody-Based Cancer Immunotherapy

Allison G. Roy, J. Michael Robinson, Prannda Sharma, Alba Rodriguez-Garcia, Mathilde A. Poussin, Cheryl Nickerson-Nutter, and Daniel J. Powell, Jr.

https://pubmed.ncbi.nlm.nih.gov/34070369

Intra-Tumoral Nerve-Tracing in a Novel Syngeneic Model of High-Grade Serous Ovarian Carcinoma.

Barr JL, Kruse A, Restaino AC, Tulina N, Stuckelberger S, Vermeer SJ, Williamson CS, Vermeer DW, Madeo M, Stamp J, Bell M, Morgan M, Yoon J-Y, Mitchell MA, Budina A, Omran DK, Schwartz LE, Drapkin R, Vermeer PD. Cells. 2021; 10(12):3491.

https://doi.org/10.3390/cells10123491

Core Facilities Spotlight: Penn Genomics & Sequencing Core - RRID:SCR_024999

Director: Tapan Ganguly, PhD (gangulyt@pennmedicine.upenn.edu)

Technical Director: Erik Toorens (toorens@pennmedicne.upenn.edu)

Bioinformatics: John Tobias, PhD (jtobias@pennmedicne.upenn.edu)

Services offered (please note Sanger sequencing has been discontinued)

It’s all based on full service Next-Generation Sequencing (NGS): both short read and long read, starting from consultation, DNA/RNA extraction, library prep, sequencing to bioinformatics.

1. Project Consultation and Help with Design

2.  Short Read: Illumina Platforms- MiSeq, NextSeq 2000, NovaSeq X Plus

• MPG project (WGS)
• Targeted Gene Panel sequencing
• RNA-Seq (mRNA and total)
• Small RNA-Seq
• 10X Single Cell and single nuclei RNA-Seq
• ChIP-Seq, CUT & RUN, ATAC-Seq
• Introducing Multiome (scRNA-Seq+scATAC-Seq)
• Sequencing of client provided libraries

3. Long-Read: PacBio Revio

• WGS
• Human Virome Project
• About to start RNA sequencing, Fiber-Seq and other applications

3.  Long-Read: Library prep and Sequencing on ONT MinION & PrometheION 

4. Bioinformatics 

5.  DNA/RNA extraction from various source

6.  NGS QC services including:

• BioAnalyzer for fragment sizing
• Quantitation by Qubit 
• qPCR for library quantitation, also small scale project for genotyping and gene expression
• Femto Pulse & TapeStation for fragment sizing needed for long read sequencing
• BluePippin for DNA size selection

Have you used any core products, services or facilities?

We encourage you to complete a survey to provide us feedback on your experience.

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