bluuebunny/crossref_metadata_2025 huggingface dataset:
Supplementary Figure S17 from Phase I Study of Elraglusib (9-ING-41), a Glycogen Synthase Kinase-3β Inhibitor, as Monotherapy or Combined with Chemotherapy in Patients with Advanced Malignancies
Authors: Carneiro Benedito A. , Cavalcante Ludimila , Mahalingam Devalingam , Saeed Anwaar , Safran Howard , Ma Wen Wee , Coveler Andrew L. , Powell Steven , Bastos Bruno , Davis Elizabeth , Sahai Vaibhav , Mikrut William , Longstreth James , Smith Sheri , Weisskittel Taylor , Li Hu , Borden Brittany A. , Harvey R. Donald , Sahebjam Solmaz , Cervantes Andrés , Koukol Austin , Mazar Andrew P. , Steeghs Neeltje , Kurzrock Razelle , Giles Francis J. , Munster Pamela
Published: February 2024

Best Overall Response by Cancer Histology in Part 1
Supplementary Figure S16 from Phase I Study of Elraglusib (9-ING-41), a Glycogen Synthase Kinase-3β Inhibitor, as Monotherapy or Combined with Chemotherapy in Patients with Advanced Malignancies
Authors: Carneiro Benedito A. , Cavalcante Ludimila , Mahalingam Devalingam , Saeed Anwaar , Safran Howard , Ma Wen Wee , Coveler Andrew L. , Powell Steven , Bastos Bruno , Davis Elizabeth , Sahai Vaibhav , Mikrut William , Longstreth James , Smith Sheri , Weisskittel Taylor , Li Hu , Borden Brittany A. , Harvey R. Donald , Sahebjam Solmaz , Cervantes Andrés , Koukol Austin , Mazar Andrew P. , Steeghs Neeltje , Kurzrock Razelle , Giles Francis J. , Munster Pamela
Published: February 2024

Overall Survival by Cancer Histology in Part 1
Supplementary Table 4 from Neoadjuvant Selicrelumab, an Agonist CD40 Antibody, Induces Changes in the Tumor Microenvironment in Patients with Resectable Pancreatic Cancer
Authors: Byrne Katelyn T. , Betts Courtney B. , Mick Rosemarie , Sivagnanam Shamilene , Bajor David L. , Laheru Daniel A. , Chiorean E. Gabriela , O'Hara Mark H. , Liudahl Shannon M. , Newcomb Craig , Alanio Cécile , Ferreira Ana P. , Park Byung S. , Ohtani Takuya , Huffman Austin P. , Väyrynen Sara A. , Dias Costa Andressa , Kaiser Judith C. , Lacroix Andreanne M. , Redlinger Colleen , Stern Martin , Nowak Jonathan A. , Wherry E. John , Cheever Martin A. , Wolpin Brian M. , Furth Emma E. , Jaffee Elizabeth M. , Coussens Lisa M. , Vonderheide Robert H.
Published: February 2024

Table S4 summarizes the statistical analyses of mIHC data based on ROI location or treatment cohort.
Data from Intratumoral Delivery of Chimeric Antigen Receptor T Cells Targeting CD133 Effectively Treats Brain Metastases
Authors: Kieliszek Agata M. , Mobilio Daniel , Upreti Deepak , Bloemberg Darin , Escudero Laura , Kwiecien Jacek M. , Alizada Zahra , Zhai Kui , Ang Patrick , Chafe Shawn C. , Vora Parvez , Venugopal Chitra , Singh Sheila K.
Published: February 2024

AbstractPurpose:
Brain metastases (BM) are mainly treated palliatively with an expected survival of less than 12 months after diagnosis. In many solid tumors, the human neural stem cell marker glycoprotein CD133 is a marker of a tumor-initiating cell population that contributes to therapy resistance, relapse, and metastasis.
Experimental Design:
Here, we use a variant of our previously described CD133 binder to generate second-generation CD133-specific chimeric antigen receptor T cells (CAR-T) to demonstrate its specificity and efficacy against multiple patient-derived BM cell lines with variable CD133 antigen expression.
Results:
Using both lung- and colon-BM patient-derived xenograft models, we show that a CD133-targeting CAR-T cell therapy can evoke significant tumor reduction and survival advantage after a single dose, with complete remission observed in the colon-BM model.
Conclusions:
In summary, these data suggest that CD133 plays a critical role in fueling the growth of BM, and immunotherapeutic targeting of this cell population is a feasible strategy to control the outgrowth of BM tumors that are otherwise limited to palliative care.

See related commentary by Sloan et al., p. 477
Data from Impact of Rare Structural Variant Events in Newly Diagnosed Multiple Myeloma
Authors: Chojnacka Monika , Diamond Benjamin , Ziccheddu Bachisio , Rustad Even , Maclachlan Kylee , Papadimitriou Marios , Boyle Eileen M. , Blaney Patrick , Usmani Saad , Morgan Gareth , Landgren Ola , Maura Francesco
Published: February 2024

AbstractPurpose:
Whole-genome sequencing (WGS) of patients with newly diagnosed multiple myeloma (NDMM) has shown recurrent structural variant (SV) involvement in distinct regions of the genome (i.e., hotspots) and causing recurrent copy-number alterations. Together with canonical immunoglobulin translocations, these SVs are recognized as “recurrent SVs.” More than half of SVs were not involved in recurrent events. The significance of these “rare SVs” has not been previously examined.
Experimental Design:
In this study, we utilize 752 WGS and 591 RNA sequencing data from patients with NDMM to determine the role of rare SVs in myeloma pathogenesis.
Results:
Ninety-four percent of patients harbored at least one rare SV event. Rare SVs showed an SV class-specific enrichment within genes and superenhancers associated with outlier gene expression. Furthermore, known myeloma driver genes recurrently impacted by point mutations were dysregulated by rare SVs.
Conclusions:
Overall, we demonstrate the association of rare SVs with aberrant gene expression supporting a potential driver role in myeloma pathogenesis.
Supplementary figure 7 from Design and Evaluation of Phosphonamidate-Linked Exatecan Constructs for Highly Loaded, Stable, and Efficacious Antibody–Drug Conjugates
Authors: Schmitt Saskia , Machui Paul , Mai Isabelle , Herterich Sarah , Wunder Swetlana , Cyprys Philipp , Gerlach Marcus , Ochtrop Philipp , Hackenberger Christian P.R. , Schumacher Dominik , Helma Jonas , Vogl Annette M. , Kasper Marc-André
Published: February 2024

Exatecan, DXd, Enhertu and trastuzumab-LP5 induce immunogenic cell death. Immunogenic cell death induced by exatecan, DXd, trastuzumab-LP5 DAR 8 and Enhertu. HER2-positive SKBR-3 and N-87 cells were treated for indicated time points with 20 nM of respective free payloads and ADCs. As markers for immunogenic cell death, ATP and HMGB1 release into the supernatant as well as calreticulin exposure on the cell surface were determined. Therefore, cells were stained with live/dead stain and anti-calreticulin and analyzed by flow cytometry. ATP and HMGB1 release into the supernatant were measured by luminescence-based readouts. Graphs show means of n = 2 ± SEM.
Supplementary figure 4 from Design and Evaluation of Phosphonamidate-Linked Exatecan Constructs for Highly Loaded, Stable, and Efficacious Antibody–Drug Conjugates
Authors: Schmitt Saskia , Machui Paul , Mai Isabelle , Herterich Sarah , Wunder Swetlana , Cyprys Philipp , Gerlach Marcus , Ochtrop Philipp , Hackenberger Christian P.R. , Schumacher Dominik , Helma Jonas , Vogl Annette M. , Kasper Marc-André
Published: February 2024

Optimization of the conjugation reaction of an antibody with LP5. A) Variation of equivalents of 3 and TCEP in the conjugation reaction and analysis of the DAR by MS. Constant conditions: 10 mg/mL antibody, buffer at pH 8.3, 16 hours. B) Variation of the pH in the conjugation reaction and analysis of the DAR by MS over the course of 24 hours. Constant conditions: 10 mg/mL antibody, 10 equivalents of LP5 with respect to the mAb, 5 eq. of TCEP.
ADC characterization from Design and Evaluation of Phosphonamidate-Linked Exatecan Constructs for Highly Loaded, Stable, and Efficacious Antibody–Drug Conjugates
Authors: Schmitt Saskia , Machui Paul , Mai Isabelle , Herterich Sarah , Wunder Swetlana , Cyprys Philipp , Gerlach Marcus , Ochtrop Philipp , Hackenberger Christian P.R. , Schumacher Dominik , Helma Jonas , Vogl Annette M. , Kasper Marc-André
Published: February 2024

Characterization Data on the antibodies and antibody-drug-conjugates.
Supplementary Table S7-1 from Novel Methionine Aminopeptidase 2 Inhibitor M8891 Synergizes with VEGF Receptor Inhibitors to Inhibit Tumor Growth of Renal Cell Carcinoma Models
Authors: Friese-Hamim Manja , Ortiz Ruiz Maria J. , Bogatyrova Olga , Keil Marina , Rohdich Felix , Blume Beatrix , Leuthner Birgitta , Czauderna Frank , Hahn Diane , Jabs Julia , Jaehrling Frank , Heinrich Timo , Kellner Roland , Chan Katherine , Tong Amy H.Y. , Wienke Dirk , Moffat Jason , Blaukat Andree , Zenke Frank T.
Published: February 2024

Bayes Factor (BF) scores of MetAP1 and MetAP2 in the screens
Supplementary Figure S5-1 from Novel Methionine Aminopeptidase 2 Inhibitor M8891 Synergizes with VEGF Receptor Inhibitors to Inhibit Tumor Growth of Renal Cell Carcinoma Models
Authors: Friese-Hamim Manja , Ortiz Ruiz Maria J. , Bogatyrova Olga , Keil Marina , Rohdich Felix , Blume Beatrix , Leuthner Birgitta , Czauderna Frank , Hahn Diane , Jabs Julia , Jaehrling Frank , Heinrich Timo , Kellner Roland , Chan Katherine , Tong Amy H.Y. , Wienke Dirk , Moffat Jason , Blaukat Andree , Zenke Frank T.
Published: February 2024

Treatment of three cell lines (bEND3, HT1080, HCT116) with MetAP2 inhibitors 1E−07 M TNP-470 or 1E−06 M A-832234 for 48 hours followed by IEF mobility shift separation of extracted protein lysates (lanes 1, 5, 9: protein marker).
Supplementary Figure 1 from TAS0612, a Novel RSK, AKT, and S6K Inhibitor, Exhibits Antitumor Effects in Preclinical Tumor Models
Authors: Ichikawa Koji , Ito Satoshi , Kato Emi , Abe Naomi , Machida Takumitsu , Iwasaki Junya , Tanaka Gotaro , Araki Hikari , Wakayama Kentaro , Jona Hideki , Sugimoto Tetsuya , Miyadera Kazutaka , Ohkubo Shuichi
Published: February 2024

Supplementary Figure 1. Body weight change of each treatment group corresponding to each efficacy study shown in Fig. 6B-6E are shown in panel A-D, respectively. In all studies, there was no evidence of intolerance, such as rapid and severe weight reduction. The weight on Day 0 was defined as 100%, and the increase or decrease in weight of each group on each measurement day relative to the weight on Day 0 is shown as a percentage (mean ± standard error).
Supplementary Table 2 from An Antibody–Drug Conjugate Directed to Tissue Factor Shows Preclinical Antitumor Activity in Head and Neck Cancer as a Single Agent and in Combination with Chemoradiotherapy
Authors: Bakema Jantine E. , Stigter-van Walsum Marijke , Harris Jeffrey R. , Ganzevles Sonja H. , Muthuswamy Anantharaman , Houtkamp Mischa , Plantinga Theo S. , Bloemena Elisabeth , Brakenhoff Ruud H. , Breij Esther C.W. , van de Ven Rieneke
Published: February 2024

IC50 values in vitro killing assays
Supplementary Figure S1 from An Antibody–Drug Conjugate Directed to Tissue Factor Shows Preclinical Antitumor Activity in Head and Neck Cancer as a Single Agent and in Combination with Chemoradiotherapy
Authors: Bakema Jantine E. , Stigter-van Walsum Marijke , Harris Jeffrey R. , Ganzevles Sonja H. , Muthuswamy Anantharaman , Houtkamp Mischa , Plantinga Theo S. , Bloemena Elisabeth , Brakenhoff Ruud H. , Breij Esther C.W. , van de Ven Rieneke
Published: February 2024

Schematic scheme of in vivo experiments
Figure S3 from SKP2 Knockout in Rb1/p53–Deficient Mouse Models of Osteosarcoma Induces Immune Infiltration and Drives a Transcriptional Program with a Favorable Prognosis
Authors: Ferrena Alexander , Wang Jichuan , Zhang Ranxin , Karadal-Ferrena Burcu , Al-Hardan Waleed , Singh Swapnil , Borjihan Hasibagan , Schwartz Edward L. , Zhao Hongling , Oktay Maja H. , Yang Rui , Geller David S. , Hoang Bang H. , Zheng Deyou
Published: February 2024

Osteoclast and osteoblast marker expression and principal component analysis of TKO and DKO samples.
Abstract A001: Transcriptomic and microRNA profiling revealed novel therapeutic targets for breast cancer subtypes
Authors: Elango Ramesh , Vishnubalaji Radhakrishnan , Rashid Sameera , Alajez Nehad
Published: February 2024

Numerous studies suggested breast cancer (BC) from the Middle East and North Africa (MENA) to be presented at younger age with advanced tumor grade, suggesting underlying biological differences. Given the limited transcriptomic profiling data on BC from the MENA region, we performed mRNA and microRNA (miRNA) transcriptomic profiling on a local cohort of BC (n=96) from Qatar. Our data revealed the differentially expressed genes and miRNAs in relation to BC molecular subtypes (HR+, HER2+, HER2+HR+, and TNBC), tumor grade (high vs low), patients’ age (young (≤ 40) vs old (> 40)), and ethnicity (MENA vs non-MENA). Our data revealed close similarity between TNBC and HER2+, while the transcriptome of HER2+HR+ tumor was similar to that from HR+ tumors. Integrated network analysis identified complex miRNA-mRNA regulatory networks in each BC molecular subtype, in high vs low grade tumors, in tumors from young vs old, and in tumors from MENA vs non-MENA, thus implicating miRNA-mediated gene regulation as an key mechanism in shaping the transcriptome of BC. Integration of our transcriptomic data with CRISPR-Cas9 functional screen data and the Drug-Gene Interaction Database identified numerous dependencies and therapeutic vulnerabilities for each BC molecular subtype. Among those, CDC123 was functionally validated as potential therapeutic target for TNBC. Survival analyses identified mRNA and miRNA-based signatures predicative of relapse free survival (RFS), which were validated in larger BC cohorts. Our data provides comprehensive transcriptomic profiling and unraveled the miRNA-mRNA regulatory networks in BC patients from the region and identified numerous actionable gene targets, employing integrated approach. Findings from the current study have potential implications to improve the current standard-of-care for BC from the MENA as well as patients from other ethnicities.

Citation Format: Ramesh Elango, Radhakrishnan Vishnubalaji, Sameera Rashid, Nehad Alajez. Transcriptomic and microRNA profiling revealed novel therapeutic targets for breast cancer subtypes [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A001.
Abstract A033: Nuclear EGFR as a regulator of the tumor microenvironment
Authors: Escoto Angelica
Published: February 2024

Overexpression of the Epidermal Growth Factor Receptor (EGFR) is observed in all subtypes of breast cancer and is associated with large tumor size, poor differentiation, and poor clinical outcomes. However, the role of EGFR in driving the disease remains unclear, as EGFR-targeted antibodies and tyrosine kinase inhibitors fail to work effectively in breast cancer patients with EGFR overexpression. A possible explanation for therapeutic resistance is the role of intracellular EGFR, where retrograde trafficking of EGFR to the nucleus results in EGFR functioning directly as a transcriptional cofactor, regulating the expression of genes that promote tumor growth, metastasis, and an immune suppressive microenvironment. Our goal is to understand how targeting nuclear EGFR impacts this microenvironment. Using a novel therapeutic peptide (cSNX1.3) that targets retrograde trafficking of EGFR, we discovered that inhibiting retro-translocation of EGFR elicited an immune response as demonstrated by the secretion of inflammatory cytokines. Using RNA-Seq analysis, we detected an increase in the expression of cytokine receptors and natural killer (NK) cell ligands, such as RAET1 and AICL. We demonstrated that this active immune microenvironment is not observed when we treat with the EGFR kinase inhibitor Erlotinib, indicating a nuclear EGFR-specific outcome. Studies from tumor-bearing WAP-TGFα transgenic mice (an EGFR-dependent model of breast cancer) found the presence of NK cells and the expression of their activating ligands and receptors, IL-33 and SLAM7, respectively, in the tumor microenvironment. We hypothesize that nuclear EGFR is suppressing the expression of inflammatory cytokines, receptors, and ligands important for activation and recruitment of NK cells, thereby allowing immune evasion and ultimately progression of the disease. Future studies will investigate the potential to combine nuclear EGFR inhibitors with immunotherapies to activate the tumor immune microenvironment and promote optimal therapeutic efficacy.

Citation Format: Angelica Escoto. Nuclear EGFR as a regulator of the tumor microenvironment [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A033.
Abstract A047: Gamma Aminobutyric Acid Subunit Pi (GABRP) Promotes Breast Cancer Metastasis to the Brain
Authors: Packard Rebecca
Published: February 2024

Triple negative breast cancer (TNBC) is an aggressive subset of breast cancer associated with poor prognosis. Although TNBC is only responsible for about 10-15% of breast cancer cases, it accounts for nearly 37% of mortalities. A main factor resulting in this poor prognosis is a higher risk of rapid relapse, which is distant metastasis or death within two years of diagnosis, compared to other breast cancer subsets. To begin to tease out mechanisms of this TNBC-specific rapid relapse, we analyzed differential expression between those tumors resulting in rapid relapse versus those tumors with delayed relapse. This analysis was completed in two independent microarray datasets and revealed a significant upregulation of gamma aminobutyric acid subunit pi (GABRP) mRNA in the TNBC tumors that rapidly relapsed. Previous work by us and others has revealed GABRP as a driver of aggressive behaviors in TNBC cell lines; however, its role in metastatic recurrence is still unclear. We have also observed a correlation between high GABRP mRNA and preferential metastatic progression to the brain. Thus, we hypothesized GABRP is a key mediator of metastasis in aggressive TNBCs, specifically in the establishment of brain metastases. To date, we have completed preliminary in vivo experimental metastasis studies of human breast cancer cells with and without GABRP expression where loss of GABRP reduces brain metastasis. Ongoing studies aim to test metastatic progression in a spontaneous metastasis in vivo model. We are also optimizing an antibody for biomarker screening in patients. Combined, our studies provide strong evidence that GABRP is a major driver of brain-specific metastases and subsequent poorer outcomes associated with TNBC, suggesting targeting GABRP has high therapeutic potential to reduce metastasis and mortality in TNBC patients.

Citation Format: Rebecca Packard. Gamma Aminobutyric Acid Subunit Pi (GABRP) Promotes Breast Cancer Metastasis to the Brain [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr A047.
Abstract B002: The impact of mir-4728 on translation and pathway regulation in HER2-amplified breast cancer
Authors: Hafstad Völundur , Han Euisuk , Persson Helena
Published: February 2024

MicroRNAs (miRNAs) are a class of small non-coding RNAs that have been implicated in cancer. Our research focuses on the miRNA mir-4728, which is located in an intron in the HER2 locus. The HER2 locus is amplified in approximately 15% of all breast tumors and is associated with a poor prognosis. Current therapeutic strategies for HER2-positive tumors involve targeted inhibition of the HER2 protein with monoclonal antibodies such as trastuzumab in combination with chemotherapy and surgery. However, if mir-4728 has a function independent of its host gene, targeting the HER2 protein alone may be insufficient. To investigate the role of mir-4728, we utilized antisense oligonucleotides to specifically block mir-4728 in a HER2-amplified breast cancer cell line, while leaving the protein receptor in tact. Polysome fractionation and ribosome profiling revealed that blocking the miRNA resulted in a substantial change in protein translation. We hypothesize that this effect may come as a result of mir-4728 being an indirect regulator of EIF4A, a key factor in the initiation of translation. In addition, we have observed changes in the synthesis of aromatase, a crucial enzyme in estrogen synthesis. These findings suggest that mir-4728 may play a role in the regulation of multiple pathways that contribute to cancer progression. Further investigation into this mechanism may provide valuable insight into the development of new therapeutic strategies for cancer treatment.

Citation Format: Völundur Hafstad, Euisuk Han, Helena Persson. The impact of mir-4728 on translation and pathway regulation in HER2-amplified breast cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr B002.
Abstract IA06: Postpartum breast involution informs breast cancer metastasis to the liver
Authors: Schedin Pepper
Published: February 2024

Young women with breast cancer have disproportionally higher rates of metastasis, and effective treatment strategies are lacking. Our lab has focused on investigating how normal reproductive changes in tissue biology interface with breast cancer metastasis in young patients. These studies identify weaning-induced involution of the breast as a tissue remodeling process similar to wound healing that promotes metastasis in rodent models. Relevance to women is suggested by the fact that a breast cancer diagnosis within 5 years of childbirth is a strong and independent risk factor for metastasis. Further, these studies find that up to 50% of all young onset breast cancer is diagnosed within this high risk postpartum window. This subset of common, young onset breast cancer is referred to as postpartum breast cancer (PPBC). We find that PPBC appears durably altered by involution, as PPBC tumors display involution, metastatic, and treatment resistant molecular signatures. PPBC also specifically associates with increased liver metastases, a metastatic site associated with very poor prognosis. In rodents, we identified a functional link between the mammary gland and the liver, including weaning-induced liver involution. Liver involution is characterized by hepatocyte cell death, fibroblast activation, ECM deposition, and an immune regulatory infiltrate similar to that found in the postpartum involuting breast. In rodent models of breast cancer liver metastasis (BCLM), the involuting liver supports outgrowth of circulating breast cancer cells more than the nulliparous host liver. Evidence for similar liver biology occurring in women is suggested by studies in healthy women, where we find liver volume increase during pregnancy and loss post wean, data consistent with liver involution. In our mouse models of BCLM, the involution metastatic advantage coincided with weaning-induced immune tolerance in the liver. We next targeted the pro-tumor, immune suppressed state of involution with the immune modulatory agent vitamin D. These studies revealed dramatic down regulation of liver metabolism with weaning, including liver cytochrome P450 enzymes, which effectively nullified the protective effect of vitamin D in involution hosts. Combined, these novel findings are anticipated to have implications for sex-specific liver diseases broadly, efficacy of pro-drugs in the postpartum window, and for breast cancer outcomes in young patients.

Citation Format: Pepper Schedin. Postpartum breast involution informs breast cancer metastasis to the liver [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Breast Cancer Research; 2023 Oct 19-22; San Diego, California. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_1):Abstract nr IA06.
Abstract B008: The polyclonal path towards malignant transformation in familial adenomatous polyposis
Authors: Schenck Ryan O. , Khan Aziz , Horning Aaron M. , Esplin Edward D. ,   HTAN Consortia, Greenleaf William J. , Ford James M. , Snyder Michael P. , Curtis Christina
Published: February 2024

The widely accepted paradigm that cancer initiation is a monoclonal event has not been definitively resolved. This is largely due to the limitations of experimental systems to study cancer initiation, a definitively transient step in tumorigenesis. Individuals with familial adenomatous polyposis (FAP) possess a germline APC mutation, leading to hundreds of colonic polyps in adolescence and an eventual 100% lifetime risk of colorectal cancer. As such, total colectomies are performed once polyp burden becomes unmanageable and provide the resected colons from FAP donors provide a source of histologically normal mucosa, benign and dysplastic polyps, and, on rare occasions, adenocarcinomas, and serve as an exemplary model disease to understand human tumorigenesis. Through whole genome sequencing of 123 independent samples from six patients, we reveal the polyclonal origins of tumorigenesis in FAP. We characterize and contrast the genomic landscape and relative timing of driver mutation acquisition across normal to dysplastic and invasive colon tissue and compare this with multi-region sequencing data from sporadic colorectal cancers (CRC). We find that only early sporadic CRC drivers are common across the more heterogeneous premalignant stages. Selection, as assessed based on the ratio of nonsynonymous to synonymous mutations (dN/dS), is higher in benign than dysplastic FAP lesions and in sporadic adenomas relative to carcinomas. Phylogenetic reconstruction and pairwise sample comparisons reveal extensive heterogeneity and subclonal sharing within a patient’s benign and dysplastic lesions. Using a mechanistic mathematical model, we infer polyclonality for 90-100% of benign and 53-83% of dysplastic samples. Based on these findings, we propose a conceptual framework for the polyclonal origin of intestinal malignancies where inconsequential mutations, arising during colon formation in utero, are present across the colon and are valuable markers to uncover polyclonal ancestry.

Citation Format: Ryan O. Schenck, Aziz Khan, Aaron M. Horning, Edward D. Esplin, HTAN Consortia, William J. Greenleaf, James M. Ford, Michael P. Snyder, Christina Curtis. The polyclonal path towards malignant transformation in familial adenomatous polyposis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B008.
Abstract B013: Development of oropharyngeal tumor organoids for disease modeling and high throughput drug screening
Authors: Bommakanti Krishna K. , Lin Luda , Alhiyari Yazeed , Sannajust Andreanne , Mo Brandon , Evans Lauran , Tebon Peyton , John Maie St. , Soragni Alice
Published: February 2024

Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide with approximately 550,000 new cases diagnosed each year. The oropharynx is one of the most common sites of occurrence, and disease in this region most often presents in the palatine tonsil, followed by the base of tongue and soft palate. Human papilloma virus (HPV) is a common cause of HNSCC, giving rise to a distinct subset of tumors with a different clinical presentation, disease course, and response to treatment. In order to further characterize HPV+ HNSCC tumors and their therapy response, we have leveraged our high throughput 3D tumor organoid screening platform. Our approach entails seeding tumor cells in extracellular matrix gels deposited around the perimeter of tissue culture wells in ring-like structures, with screening results available within a week from surgery (Phan et al, 2019; Al Shihabi et al, 2022; Nguyen et al, 2022; Al Shihabi et al 2023). We particularly focused on tonsil tumors, and develop organoids from both HNSCC and contralateral normal tonsil tissue. Thus far, we have procured tonsil samples from 31 patients to develop organoids, perform high throughput drug screening, and immunohistochemical characterization including H&E staining, Ki67, p16 and p53 immunohistochemical staining. We have leveraged dynamic optical contrast imaging (DOCI), a label-free tissue autofluorescence imaging method that is being investigated clinically (Kim et al, 2017), to assist in distinguishing tumor organoids from normal tissue organoids. Lastly, given the importance of radiation as a treatment modality for HPV+ HNSCC, we have also optimized a chemoradiation pipeline to test possible combinatorial effects. Taken together, our results demonstrate that 3D organoids of HNSCC generated from patient samples can successfully preserve native tissue characteristics and can be used for high throughput drug screening and radiation de-escalation testing, affording critical insight into the management of HNSCC in patients.

Citation Format: Krishna K. Bommakanti, Luda Lin, Yazeed Alhiyari, Andreanne Sannajust, Brandon Mo, Lauran Evans, Peyton Tebon, Maie St. John, Alice Soragni. Development of oropharyngeal tumor organoids for disease modeling and high throughput drug screening [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B013.
Abstract B029: Centuries of genome instability and evolution in soft-shell clam (Mya arenaria) transmissible cancer
Authors: Hart Samuel F.M. , Metzger Michael J.
Published: February 2024

Transmissible cancers are infectious parasitic clones that metastasize to new hosts, living past the death of the founder animal in which the cancer initiated. Using genomic and transcriptomic analyses, we investigated the evolutionary history of a recently identified transmissible cancer lineage that has spread though the soft-shell clam (Mya arenaria) population. We first assembled a chromosome-scale soft-shell clam reference genome and characterized somatic mutations in the cancer lineage, discovering a novel mutational signature that estimates the lineage to be >200 years old and observing a wide variety of mutation types indicative of an extremely unstable cancer genome. We next quantified gene expression, observing differential expression of stereotypical cancer hallmarks in addition to key pathways that may have facilitated the cancer’s ability to survive seawater transfer to new hosts and evade immune rejection. Finally, we developed genetic assays to track bivalve transmissible neoplasia in the soft-shell clam and identify a novel lineage in the Baltic clam (Macoma balthica). Taken together, this study reveals the long-term survival of an invertebrate cancer lineage and identifies adaptive mechanisms to evade physical and immune barriers to cancer transmission, which may have been facilitated in part by the adaptive potential of its unstable genome.

Citation Format: Samuel F.M. Hart, Michael J. Metzger. Centuries of genome instability and evolution in soft-shell clam (Mya arenaria) transmissible cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr B029.
Abstract IA014: Detecting epistatic effects among somatic cancer mutations across oncogenesis
Authors: Alfaro-Murillo Jorge A. , Dasari Krishna , Townsend Jeffrey P.
Published: February 2024

The somatic evolution of cancer depends on the rate at which new mutations are acquired, as well as the selective pressure acting on them. Further, mutual exclusivity or co-occurrence of somatic variants suggests that current somatic variants can exert antagonistic or synergistic epistatic effects on the selection of new mutations, contributing to a complex landscape of evolutionary trajectories. However, quantifying these epistatic effects—which are essential to estimation of the trajectory of likely cancer genotoypes—has been a challenge, especially for higher-order epistatic effects. To estimate these epistatic effects, we have developed a continuous-time Markov chain model that enables the estimation of mutation origination and fixation, dependent on somatic cancer genotype. Coupling the continuous-time Markov chain model with a mutation-rate deconvolution approach, we have estimated the underlying mutation rates and selection intensities across trajectories of oncogenesis. Specifically, we report the mutation rates, selection intensities, and consequent variant fluxes for lung adenocarcinoma, informed by a compilation of samples from multiple data sets including The Cancer Genome Atlas and the AACR Project GENIE. Furthermore, we compare smoker and nonsmoker tumor cohorts describing the distinct evolutionary trajectories jointly, influenced by differential mutation and also by the differential physiological effects that smoking can have on the selective regime of lung tissue. Our approach enables inference of the most likely routes of site-specific variant evolution, as well as estimation of the selection strength operating on each step along the route—a key component of what we need to know to prioritize, develop, and implement personalized cancer therapies.

Citation Format: Jorge A. Alfaro-Murillo, Krishna Dasari, Jeffrey P. Townsend. Detecting epistatic effects among somatic cancer mutations across oncogenesis [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr IA014.
Abstract IA016: Bayesian phylodynamics to quantify cancer growth across space and time
Authors: Lewinsohn Maya , Bedford Trevor , Müller Nicola F. , Feder Alison
Published: February 2024

Phylogenetics has traditionally inferred shared genetic histories of species over macroevolutionary time. With the expansion of cancer multi-region and single-cell sequencing, phylogenetic approaches have found new uses mapping the evolutionary histories of tumors as well. Recently developed “phylodynamic” methods that integrate phylogenetic and population dynamic modeling offer further promise - uncovering cancer growth dynamics from the topologies and branch lengths of tumor trees. Here, I discuss two recent efforts in this area: 1) Heterogeneous growth rates across a tumor become encoded in the branching patterns of phylogenetic trees built from multi-region sequencing. We introduce a cancer-specific extension to a class of multi-state birth-death models to infer these growth rate differences across space. We apply our model (SDevo) to a sample of hepatocellular carcinomas and infer that these tumor peripheries grow 2-6 times faster than their interiors. 2) Tumors experience differential growth rates over time as they acquire new driver mutations and invade their surrounding tissues, and these growth dynamics similarly leave characteristic signatures in their phylogenies. We employ Bayesian skyline models to dissect tumor growth dynamics from a dataset of diverse cancers and reveal variation in cancer growth rates over time. As cancer sequencing continues to proliferate, phylodynamic approaches are poised to reveal new quantitative insights into cancer growth dynamics across time and space.

Citation Format: Maya Lewinsohn, Trevor Bedford, Nicola F. Müller, Alison Feder. Bayesian phylodynamics to quantify cancer growth across space and time [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Translating Cancer Evolution and Data Science: The Next Frontier; 2023 Dec 3-6; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(3 Suppl_2):Abstract nr IA016.
Supplementary Figure 7 from ORAOV1, CCND1, and MIR548K Are the Driver Oncogenes of the 11q13 Amplicon in Squamous Cell Carcinoma
Authors: Mahieu Céline I. , Mancini Andrew G. , Vikram Ellee P. , Planells-Palop Vicente , Joseph Nancy M. , Tward Aaron D.
Published: February 2024

Expression analysis of TXN and in vivo tumors
Supplementary Figure 4 from ORAOV1, CCND1, and MIR548K Are the Driver Oncogenes of the 11q13 Amplicon in Squamous Cell Carcinoma
Authors: Mahieu Céline I. , Mancini Andrew G. , Vikram Ellee P. , Planells-Palop Vicente , Joseph Nancy M. , Tward Aaron D.
Published: February 2024

Development of a novel primary keratinocyte cell engineering workflow
Supplementary Figure 3 from ORAOV1, CCND1, and MIR548K Are the Driver Oncogenes of the 11q13 Amplicon in Squamous Cell Carcinoma
Authors: Mahieu Céline I. , Mancini Andrew G. , Vikram Ellee P. , Planells-Palop Vicente , Joseph Nancy M. , Tward Aaron D.
Published: February 2024

Growth analyses upon abrogation of MIR548K
Supplementary Figure 3 from Spatial Transcriptomics Suggests That Alterations Occur in the Preneoplastic Breast Microenvironment of BRCA1/2 Mutation Carriers
Authors: Caputo Anthony , Vipparthi Kavya , Bazeley Peter , Downs-Kelly Erinn , McIntire Patrick , Duckworth Lauren A. , Ni Ying , Hu Bo , Keri Ruth A. , Karaayvaz Mihriban
Published: February 2024

Human breast epithelial cell cultures
Supplementary Materials and Methods from PKCδ Regulates Chromatin Remodeling and DNA Repair through SIRT6
Authors: Affandi Trisiani , Haas Ami , Ohm Angela M. , Wright Gregory M. , Black Joshua C. , Reyland Mary E.
Published: February 2024

TCGA analysis
Supplementary figure 7 from Mitochondrial Translocase TOMM22 Is Overexpressed in Pancreatic Cancer and Promotes Aggressive Growth by Modulating Mitochondrial Protein Import and Function
Authors: Haastrup Mary Oluwadamilola , Vikramdeo Kunwar Somesh , Anand Shashi , Khan Mohammad Aslam , Carter James Elliot , Singh Seema , Singh Ajay Pratap , Dasgupta Santanu
Published: February 2024

This file contains supplementary figure 7 and its figure legend
Supplementary figure 5 from Mitochondrial Translocase TOMM22 Is Overexpressed in Pancreatic Cancer and Promotes Aggressive Growth by Modulating Mitochondrial Protein Import and Function
Authors: Haastrup Mary Oluwadamilola , Vikramdeo Kunwar Somesh , Anand Shashi , Khan Mohammad Aslam , Carter James Elliot , Singh Seema , Singh Ajay Pratap , Dasgupta Santanu
Published: February 2024

This file contains supplementary figure 5 and its figure legend
Supplementary figure 4 from Mitochondrial Translocase TOMM22 Is Overexpressed in Pancreatic Cancer and Promotes Aggressive Growth by Modulating Mitochondrial Protein Import and Function
Authors: Haastrup Mary Oluwadamilola , Vikramdeo Kunwar Somesh , Anand Shashi , Khan Mohammad Aslam , Carter James Elliot , Singh Seema , Singh Ajay Pratap , Dasgupta Santanu
Published: February 2024

This file contains supplementary figure 4 and its figure legend
Supplementary Materials and Methods from SOX10 Loss Sensitizes Melanoma Cells to Cytokine-Mediated Inflammatory Cell Death
Authors: Rosenbaum Sheera R. , Caksa Signe , Stefanski Casey D. , Trachtenberg Isabella V. , Wilson Haley P. , Wilski Nicole A. , Ott Connor A. , Purwin Timothy J. , Haj Jelan I. , Pomante Danielle , Kotas Daniel , Chervoneva Inna , Capparelli Claudia , Aplin Andrew E.
Published: February 2024

Materials and Methods for Supplementary Figures
Supplementary Figure 3 from Integrating Clinical Cancer and PTM Proteomics Data Identifies a Mechanism of ACK1 Kinase Activation
Authors: Balasooriya Eranga R. , Madhusanka Deshan , López-Palacios Tania P. , Eastmond Riley J. , Jayatunge Dasun , Owen Jake J. , Gashler Jack S. , Egbert Christina M. , Bulathsinghalage Chanaka , Liu Lu , Piccolo Stephen R. , Andersen Joshua L.
Published: February 2024

ACK1 frameshift mutatants have similar RNA expression levels as ACK1 WT.
Data from Exosomal lncRNA NEAT1 Inhibits NK-Cell Activity to Promote Multiple Myeloma Cell Immune Escape via an EZH2/PBX1 Axis
Authors: Wang Qing-Ming , Lian Guang-Yu , Sheng Su-Mei , Xu Jing , Ye Long-Long , Min Chao , Guo Shu-Fang
Published: February 2024

Abstract
Exosomal long noncoding RNAs (lncRNA) derived from cancer cells are implicated in various processes, including cancer cell proliferation, metastasis, and immunomodulation. We investigated the role and underlying mechanism of exosome-transmitted lncRNA NEAT1 in the immune escape of multiple myeloma cells from natural killer (NK) cells. Multiple myeloma cells and samples from patients with multiple myeloma were obtained. The effects of multiple myeloma cell-derived exosomes (multiple myeloma exosomes) and exosomal NEAT1 on the functions of NK cells were evaluated using EdU staining, CCK-8, flow cytometry, and ELISA. Chromatin and RNA immunoprecipitation were performed to identify interactions between NEAT1, enhancer of Zeste Homolog 2 (EZH2), and pre-B-cell leukemia transcription factor 1 (PBX1). A xenograft tumor model was constructed to verify the effects of exosomal NEAT1 on tumor growth. qRT-PCR, Western blot analysis, and IHC were conducted to detect related genes. NEAT1 levels were upregulated in multiple myeloma tumor tissues, multiple myeloma cells, and multiple myeloma exosomes. Multiple myeloma exosomes suppressed cell proliferation, promoted apoptosis, reduced natural killer group 2, member D (NKG2D)-positive cells, and the production of TNFα) and interferon-gamma (IFN-γ) in NK cells, whereas NEAT1-silenced exosomes had little effect. NEAT1 silenced PBX1 by recruiting EZH2. PBX1 knockdown abrogated the effects of NEAT1-silenced exosomes on NK and multiple myeloma cells. NEAT1-silenced exosomes inhibited tumor growth in mice, decreased Ki67 and PD-L1, and increased NKG2D, TNFα, and IFNγ in tumor tissues. In summary, multiple myeloma cell–derived exosomal NEAT1 suppressed NK-cell activity by downregulating PBX1, promoting multiple myeloma cell immune escape. This study suggests a potential strategy for treating multiple myeloma.
Implications:
This study reveals that exosomal NEAT1 regulates EZH2/PBX1 axis to inhibit NK-cell activity, thereby promoting multiple myeloma cell immune escape, which offers a novel therapeutic potential for multiple myeloma.
Table S1 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
Authors: Napoli Marco , Deshpande Avani A. , Chakravarti Deepavali , Rajapakshe Kimal , Gunaratne Preethi H. , Coarfa Cristian , Flores Elsa R.
Published: February 2024

List of DNA oligonucleotides for the TAp63 and ∆Np63 ChIP assays
FIGURE 2 from Genome-wide p63-Target Gene Analyses Reveal TAp63/NRF2-Dependent Oxidative Stress Responses
Authors: Napoli Marco , Deshpande Avani A. , Chakravarti Deepavali , Rajapakshe Kimal , Gunaratne Preethi H. , Coarfa Cristian , Flores Elsa R.
Published: February 2024

Identification of ∆Np63 and TAp63 regulated transcriptomes. A, Unsupervised clustering of the transcriptional profiles in WT, ΔNp63−/−, and TAp63−/− epidermal cells using Pearson correlation coefficient (PCC). B, Heat map visualization of the genes affected in either ΔNp63−/− or TAp63−/− epidermal cells. C, Reciprocal gene set enrichment analysis (GSEA) of the genes induced or repressed by the indicated p63 isoform (FC 8x, FDR < 0.05).
Clinical Presentation and Molecular Characterization of 3 Patients with Vici Syndrome: Two Novel Variants in the EPG5 Gene
Authors: Selamioğlu Arzu , Doğan Burcu Yeter , Balcı Mehmet Cihan , Kalaycı Tuğba , Karaca Meryem , Ak Belkıs , Durmuş Aslı , Körbeyli Hüseyin Kutay , Gökçay Gülden
Published: February 2024

Introduction: Vici syndrome is an ultra-rare, congenital disorder of autophagy characterized by agenesis of the corpus callosum, cataracts, cardiomyopathy, combined immunodeficiency, developmental delay, and hypopigmentation. Patients usually present in the neonatal period or infancy with profound hypotonia, based on information available from the nearly 100 cases reported to date. Case Presentation: We present 3 new cases of Vici syndrome confirmed by genetic analysis of EPG5 gene. The 3 male patients had neonatal hypotonia, progressive microcephaly, psychomotor retardation, recurrent respiratory tract infections, optic atrophy, and failure to thrive, but no cataracts or hepatomegaly. Three disease-causing variants in homozygous state were detected in the EPG5 gene: two novel c.1652C>T and c.7557+2T>C forms; and one previously reported c.7447C>T. The patient, who was homozygous for the c.1652C>T mutation, presented with neonatal onset seizures that had not been reported previously. Discussion/Conclusion: The present study provides data for the evaluation of the natural history and genotype-phenotype correlations for treatment options that are expected to be available in the future.
Abstract 102: Microanatomy of Intracranial Human Thrombi by Single Nuclei Transcriptomics
Authors: Spinazzi Eleonora F , Leifer Valia P , Argenziano Michael G , Zhao Wenting , Alexander Julia E , Mahajan Aayushi , Furnari Julia L , Kotidis Corina P , Canoll Peter D , Sims Peter A , Mandigo Grace K , Connolly Edward S , Lavine Sean D
Published: February 2024

Introduction:
Microvascular dysfunction and inflammation are thought to underlie reperfusion failure following endovascular thrombectomy. Here we present the first study to produce a transcriptome-based cellular landscape of human intracranial thrombi highlighting the importance of cellular plasticity and intercellular communication at the site of occlusion.

Methods:
We performed single nuclei RNA-sequencing (snRNA-seq) on intracranial human thrombi harvested during revascularization. Unsupervised clustering, data visualization, differential expression and functional gene ontology/pathway analysis were utilized to deconvolve expression data into cell type-specific expression profiles. Thrombi snRNA-seq data were integrated with single cell RNA-seq data from symptomatic and asymptomatic human carotid plaques and healthy brain vasculature to contextualize thrombi in atherosclerotic disease, perform diffusion coefficient analysis, and identify ligand-receptor interactions.

Results:
Unbiased clustering identified six cellular populations in distinct effector states within the thrombus microenvironment. Functional gene ontology and pathway analysis revealed a monocyte subpopulation in a distinct endothelial-activation and neuroplasticity state, supporting the notion of cellular trans-differentiation and interconversion. Integration with carotid plaque data and diffusion coefficient analysis revealed shared transcriptional programs existing in a continuum, progressing from asymptomatic plaque to embolized thrombus. Ligand-receptor analysis identified macrophage mediated T-cell activation, pro-inflammatory response, immunological synapse stabilization, neuroplasticity, and monocyte trans-endothelial migration.

Conclusion:
Our novel application of snRNA-seq to thrombectomy specimens provides the highest resolution exploration of cellular differences and a best understanding of individual contextualized cell function to date. This detailed cellular landscape will facilitate mapping novel interventional targets with direct functional relevance and allow for greater personalization of post-reperfusion therapy.