In this issue:



• Announcements
• PSOM's Inaugural Frontier Core - Advanced Core for Microscopy Engineering (ACME)
• FY24 Impact: Core Resource Funding Opportunity
• ABRF Annual Meeting - March 23-26, 2025
• Save the Date: Cores Day - September 11, 2025
• High-throughput Screening Core Symposium - September 19, 2025
• Vaporizer Calibration Service for UPenn Animal Research Labs

• Core Facilities Spotlight
• Molecular Pathology and Imaging Core
• OCRC Tumor Trust
• Penn Genomic and Sequencing Core Facility (PGSC)

Announcements: PSOM's Inaugural Frontier Core - Advanced Core for Microscopy Engineering (ACME) - RRID:SCR_026289

Inspired by our strategic plan, Serving a Changing World, the Frontier Core Initiative was established to catalyze highly innovative research and transformative ideas promising to alter the trajectory of biomedical research. The initiative supports infrastructure projects not typically fundable through traditional mechanisms. By focusing on non-commercialized technologies, new methodologies, and unique collaborations, we aim to propel groundbreaking advancements in both basic and translational research. 

The Advanced Core for Microscopy Engineering will provide researchers with access to cutting-edge microscopy technologies and specialized instrumentation tailored to the unique experimental needs of our community. Additionally, the core will foster innovation by developing a library of software and hardware modules catering to a diverse range of microscopy applications. As our first Frontier Core, it will receive up to $1M in funding over three years. Please visit the Advanced Core for Microscopy Engineering (ACME) website to learn more about their exciting work. 

Announcements: FY24 Impact - Core Resource Funding Opportunity

The Core Resource Funding Opportunity is a dynamic initiative designed in support of our vital research core facilities. Below, you’ll find a glimpse of the incredible ways these funds recently propelled core facilities forward, driving exciting advancements in research. 

• Johnson Foundation Biophysics and Structural Biology Core Facility (RRID:SCR_022414):

The funding helped facilitate the purchase of proprietary software for LNP analysis by SEC-MALS, enabling the core to measure mass, RNA loading, and polydispersity. This new capability supports the LNP research community, providing data in a way that was not possible with previously existing resources.

• Path BioResource:

The funding supported the transition of Radiology Cores to the iLab/CAMS system, improving operational efficiency. The PBR IT and Admin teams facilitated a smooth transition, with SAIF staff benefiting from the enhanced software application, enabling more streamlined management of operations.

• Penn Vet Comparative Pathology Core (RRID:SCR_022438):

Funding helped the core hire veterinary pathologists, improving service quality and turnaround times. This not only boosted the core’s revenues but also provided scientific support for critical PSOM preclinical research projects, benefitting researchers across a variety of specialties.

• Rodent Metabolic Phenotyping Core – (RRID:SCR_022427):

The funds were used towards the purchase new infusion pumps, significantly increasing the core’s capacity for stable isotope infusions and hyperinsulinemic euglycemic clamps. The funding also supported staffing, allowing for a smooth transition after the loss of a technician and ensuring the core could meet the needs of 50+ faculty relying on its services.

• Tumor Tissue and BioSpecimen Bank (RRID:SCR_022430):

The funding served to support a new a Research Specialist and the purchase of a freezer to enhance tissue collection. The core successfully banked prostate cancer samples from racially diverse, high-risk patient populations, supporting groundbreaking research in CAR-T therapy, molecular and immune basis of prostate cancer, and heterogeneity in tumor types. This expanded tissue collection is critical for advancing research in areas like BRCA mutations and metastatic prostate cancer.

Announcements: ABRF Annual Meeting - March 23-26, 2025

The Association of Biomolecular Resources Facilities (ABRF) Annual Meeting is an international program that provides timely updates on cutting-edge science and its execution in a shared resource/core facility setting. These meetings also offer informative and practical workshops as well as ample networking opportunities with academics, corporate, and technology partner colleagues. This year's meeting will be held from March 23-26 in Las Vegas, and ABRF members receive a discount when registering. Please click here for more information.

If you are not yet a member, we encourage you to visit the ABRF website , and to contact April Weakley (aweakley@pennmedicine.upenn.edu) if you would like to join the organization at no charge to you via PSOM’s institutional membership. 

Announcements: Save the Date: Cores Day - September 11, 2025

We are delighted to announce Cores Day 2025! Please mark your calendars for Thursday, September 11, 2025 from 10am-1pm. The event will be again held in the Smilow lobby, this year in one consolidated shift. 

The annual Cores Day event is a joint venture with CHOP, PSOM, Penn Vet, and Wistar, in an effort to showcase the many outstanding biomedical research resources and services available throughout our campus. This event is an opportunity for students, faculty, and staff to interface with a multitude of research core facilities via informational tables staffed by core facility personnel.  

Stay tuned for more details, and we hope to see you on Thursday, September 11!  

Announcements: High-throughput Screening Core Symposium - September 19, 2025

The UPenn High-throughput Screening Core (HTSC) and the High-Throughput Institute for Discovery (HIT-ID) is hosting a symposium on Thursday September 18th, 2025 in the Gaulton Auditorium, BRB II/III from 9:00 AM to 1:00 PM and is open all faculty, postdocs, graduate students, and laboratory staff free of charge. We are delighted that Jennifer Golden, PhD from the University of Wisconsin-Madison will give the Keynote Address on development of antivirals against emerging pathogens. In addition, investigators at PENN will present their studies using high-throughput screening in basic science and drug discovery. The symposium will highlight resources and capabilities of the HTSC, and demonstrate how high-throughput screening can impact basic and translational medicine across disciplines. Program details and additional information will be available soon. Please use the QR code to register.

Announcements: Vaporizer Calibration Service for UPenn Animal Research Labs

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 Information

Weiming Bu, PhD

302 John Morgan Building

(use the Johnson Pavilion elevators) 

Weiming.Bu@pennmedicine.upenn.edu

Core Facilities Spotlight: Molecular Pathology and Imaging Core (MPIC) - RRID:SCR_022420

The Molecular Pathology & Imaging Core (MPIC) offers histological services, equipment, and expertise to assist in a variety of projects. In addition to standard processing, embedding, sectioning, and staining of tissue, MPIC is home to multiple pieces of histology equipment available for self-service use to reduce wait times and fees.

MPIC offers the following equipment & more:

• Leica Aperio Versa 8 Slide Scanner
• Leica BOND RXm Autostainer
• Laser Capture Microdissection Microscope
• X-Clarity Tissue Clearing System
• Xenium in situ Analyzer (& 3^rd party consumables and equipment)
• Visium CytAssist (& 3^rd party consumables and equipment)

Leica Aperio Versa 8

• Fluorescent and brightfield
• 5x, 10x, 20x, 40x objectives and Z-stack capabilities
• Images 8 slides at a time
• Self-service slide scanning at $50-$75 per hour depending on affiliation

Leica BOND RXm

• Automated slide stainer for consistency and efficiency
• Performs IHC and IF staining
• 30 slide capacity
• Can be used for semi-automatic spatial assays – CosMx, GeoMx, etc.
• Self-service slide staining at $6-$9 per slide depending on affiliation

For questions about MPIC’s services or equipment, email Technical Director Kate Bennett (bennk@upenn.edu) or visit our website: Molecular Pathology & Imaging Core

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



We are excited to announce that we have partnered with Pancreatic Cancer Research Center since 2022 to help launch and develop their new rapid autopsy program while we further develop and support our established program. Ultimately, we would like to have our Penn Legacy Tissue Program (PLTP) expanded to other disease/cancer sites at Penn and encourage them to engage with us without fully investing into establishing a formal program like ours. Please contact for more information.

Representative Publications:

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

Systematic analysis of CD39, CD103, CD137, and PD-1 as biomarkers for naturally occurring tumor antigen-specific TILs.

Eiva MA, Omran DK, Chacon JA, Powell DJ Jr.

Eur J Immunol. 2021 Sep 10. doi: 10.1002/eji.202149329. Epub ahead of print.

https://pubmed.ncbi.nlm.nih.gov/34505280/

CAR-T cell-mediated depletion of immunosuppressive tumor-associated macrophages promotes endogenous antitumor immunity and augments adoptive immunotherapy.

Rodriguez-Garcia A, Lynn RC, Poussin M, Eiva MA, Shaw LC, O'Connor RS, Minutolo NG, Casado-Medrano V, Lopez G, Matsuyama T, Powell DJ Jr.

Nat Commun. 2021 Feb 9;12(1):877. doi: 10.1038/s41467-021-20893-2.

https://pubmed.ncbi.nlm.nih.gov/33563975/

Inhibition of relaxin autocrine signaling confers therapeutic vulnerability in ovarian cancer.

Burston HE, Kent OA, Communal L, Udaskin ML, Sun RX, Brown KR, Jung E, Francis KE, La Rose J, Lowitz JK, Drapkin R, Mes-Masson AM, Rottapel R.

J Clin Invest. 2021 Feb 9:142677. doi: 10.1172/JCI142677.

https://pubmed.ncbi.nlm.nih.gov/33561012/

Core Facilities Spotlight: Penn Genomic and Sequencing Core Facility (PGSC) - RRID:SCR_02499

Availability of NovaSeq X Plus Sequencer and PacBio Revio at the Penn Genomics and Sequencing Core

NovaSeq X Plus

We are happy to announce that NovaSeq X Plus Sequencer has been installed at the facility and is being used for different sequencing projects. This involves, as always, from project consultation and experimental design to library preparation and QC to sequencing and bioinformatics.

Specifications:  3 flow cells - throughput 1.5B (2 lanes), 10B (8 lanes) and 25B (8 lanes) reads

Cycles - 100, 200 and 300

Cost per million read - Significantly less than NovaSeq 6000.

While we do not currently have a self-service option for the new sequencer, we are introducing a Ready to Sequence (RTS) option. In this model, you provide the library pool and sequencing reagents, as well as read geometry, loading concentration and PhiX requirements, and we will perform the sequencing as soon as we can. The turnaround time should be 1 week or less. Data distribution via BaseSpace is strongly preferred, but we can make other arrangements if this is not possible.

If you are interested in using this new option, please reach out directly to us. We will also add the relevant service items to our iLab portal in the coming days.

PacBio Revio Long-Read Sequencer

The Revio, PacBio latest high-throughput sequencer has been installed a couple of months ago and is being used for different sequencing projects. PacBio technology’s ultra-accurate HiFi long reads currently surpass Illumina’s base call accuracy.

Its applications include, but not limited to,

• Near-complete assembly of complex genomic regions
• Comprehensive detection of structural variants
• Full reconstruction of RNA isoforms and splice variants
• Determinations of epigenetic modifications 5-mC, 5hmC, 6-mA and so on
• Improved de novo assembly of diverse genomes

SPRQ Chemistry: With newly introduced SPRQ chemistry that enables 33% more reads per SMRT cells and 4-fold lower DNA requirements going into library prep, one can achieve

• 2 Human Genomes (15-20 Kb), 20X coverage on average, per SMRT cell
• 6 Transcriptomes (15-20 Kb) with Kinnex full-length transcripts,10M reads per SMRT cell
• 8 Human Methylomes (15-20 Kb), 5X coverage on average, per SMRT cell

For further information please contact:

Tapan Ganguly, Director, gangulyt@pennmedicine.upenn.edu

Erik Toorens, Technical Director, toorens@pennmedicine.upenn.edu.

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