Immortal Cell Research Articles

Establishment of primary prostate epithelial and tumorigenic cell lines using a non-viral immortalization approach

BackgroundResearch on prostate cancer is mostly performed using cell lines derived from metastatic disease, not reflecting stages of tumor initiation or early progression. Establishment of cancer cell lines derived from the primary tumor site has not been described so far. By definition, cancer cells are able to be cultured indefinitely, whereas normal epithelial cells undergo senescence in vitro. Epithelial cells can be immortalized, accomplished by using viral integration of immortalization factors. Viral approaches, however, might be impaired by regulatory and safety issues as well as random integration into regulatory genetic elements, modifying precise gene expression. We intend to use surgical specimen of prostate cancer patients to (i) prove for establishment of cancer cell lines, and (ii) perform non-viral, Sleeping Beauty (SB) transposase-based immortalization of prostate epithelial cells.MethodsRadical prostatectomy samples of prostate cancer patients (n = 4) were dissociated and cultured in vitro. Cells were cultivated either without or after non-viral, Sleeping-Beauty transposase-based stable transfection with immortalization factors SV40LT and hTERT. Established cell lines were analyzed in vitro and in vivo for characteristics of prostate (cancer) cells.ResultsInitial cell cultures without genetic manipulation underwent senescence within ≤ 15 passages, demonstrating inability to successfully derive primary prostate cancer cell lines. By using SB transposase-based integration of immortalization factors, we were able to establish primary prostate cell lines. Three out of four cell lines displayed epithelial characteristics, however without expression of prostate (cancer) characteristics, e.g., androgen receptor. In vivo, one cell line exhibited tumorigenic potential, yet characteristics of prostate adenocarcinoma were absent.ConclusionWhereas no primary prostate cancer cell line could be established, we provide for the first-time immortalization of primary prostate cells using the SB transposase system, thereby preventing regulatory and molecular issues based on viral immortalization approaches. Although, none of the newly derived cell lines demonstrated prostate cancer characteristics, tumor formation was observed in one cell line. Given the non-prostate adenocarcinoma properties of the tumor, cells have presumably undergone oncogenic transformation rather than prostate cancer differentiation. Still, these cell lines might be used as a tool for research on prostate cancer initiation and early cancer progression.

Abstract PO2-14-10: A selective MCL-1 inhibitor AZD5991 showed tumor regression in a triple-negative inflammatory breast cancer xenograft model

Abstract Background Triple-negative breast cancer (TNBC) accounts for 15-20% of all breast cancer diagnoses but up to 30% of breast cancer-related deaths. Similarly, Inflammatory breast cancer (IBC) accounts for 2-4% of breast cancer diagnosis but causes 8%–10% of all breast cancer-related deaths. The myeloid cell leukemia-1 (MCL-1) is a member of the BCL-2 family of proteins, which is highly amplified in numerous human cancers and associated with cell immortalization, transformation, and chemoresistance. In fact, MCL-1 is amplified in 55% of TNBC after preoperative chemotherapy. Amongst the MCL-1 inhibitors that have been developed, AZD5991 showed high selectivity and affinity for MCL-1. In myeloma and acute myeloid leukemia cells AZD5991 induces apoptosis and showed anti-tumor effects in in vivo models. In the present study, we evaluated the biological role of the MCL-1 inhibitor AZD5991 in IBC and TNBC in vitro and in vivo models. Materials and methods The expression of the MCL-1 gene was analyzed in the World Consortium IBC patient dataset. Next, we screened a panel of TNBC and IBC cell lines for MCL-1 expression by western blot analysis. The effect of AZD5991 on TNBC and IBC cells was analyzed via cell titer-blue proliferation, clonogenic assays and soft agar assay. To further validate these findings, we used siRNA to knockdown MCL-1 and performed cell proliferation, clonogenic and migration assays. To identify signaling pathways involved in MCL-1 Inhibitor’s effects we performed a proteome profiler human apoptosis array in TNBC cells in the presence of AZD5991. The anti-tumor effect of the MCL-1 inhibitor was evaluated using a SUM-149 (TN-IBC) orthotopic xenograft mouse model. The mice were treated with AZD5991 at doses of 15 and 30mg/kg once weekly via tail vein injection for a duration of 4 weeks. Results The mean expression level of MCL-1 was higher in patients with TNBC than in those with non-TNBC. Further, compared to the patients with ER positive, HER-2 negative tumors those with TNBC showed an increased in the mean expression of MCL-1 gene (p value= 0.05). We screened a panel of TNBC and IBC cell lines in which most of the cell lines showed high levels of MCL-1. The cell proliferation assay showed IC50 ranging from 0.27 – 19.6 μM. The SUM149, SUM190, FCIBC02, MDA-IBC3 and MDA-MB-468 cells showed high sensitivity and showed significant decrease in the proliferation rate while BCX010, KPL4, MDA-MB-231, 4T1.2 and E0771 cells as well as the normal breast cells MCF10A exhibited resistance with no significant decrease in proliferation. The clonogenic and soft agar assays with these sensitive and resistant cell lines showed similar results. Further, these findings were validated via genetic knockdown of MCL-1 which resulted in a significant decrease in cell proliferation, colony formation and migration capability of the TNBC cells. To identify signaling pathways involved in MCL-1 Inhibitor’s phenotypic changes, we performed a proteome profiler human apoptosis array which showed a decreased in BCLx expression, and an increase in expression of BAX and phospho-Rad17 proteins in the AZD5991 treated TN-IBC cells. Finally, in a SUM-149 (TN-IBC) orthotopic xenograft mouse model, mice injected with 30mg/kg showed a significant tumor regression compared to the vehicle-treated mice (vehicle vs 30 mg/kg, p value=0.0006). Conclusions and Future directions Our data demonstrates that AZD5991 inhibits tumorigenesis in an inflammatory breast cancer xenograft model. We are currently validating several significant targets to understand the biological mechanisms related to our candidate drug. Our long-term goal is to develop MCL-1 targeted therapy in combination with standard-of-care treatment for inflammatory and triple-negative breast cancers. Citation Format: Mohd Mughees, Moises Tacam, Alex Tan, Michael White, Bisrat Debeb, Emilly Villodre, Xiaoding Hu, Debu Tripathy, Wendy Woodward, Rachel Layman, Geoffrey Bartholomeusz, Chandra Bartholomeusz. A selective MCL-1 inhibitor AZD5991 showed tumor regression in a triple-negative inflammatory breast cancer xenograft model [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO2-14-10.

Angiotensin (1-7) Inhibits Transforming Growth Factor-Β1-Induced Epithelial-Mesenchymal Transition of Human Keratinocyte Hacat Cells in vitro.

Angiotensin (1-7) (Ang-(1-7)) is an emerging component of the renin-angiotensin system (RAS) with effective anti-fibrosis properties and has been shown to interfere with epithelial-mesenchymal transition (EMT) by numerous studies. In recent years, EMT has been proposed as a new therapeutic target for skin fibrotic diseases such as keloids. However, the effect of Ang-(1-7) on EMT in skin is still unclear. Hence, the purpose of this study was to explore the effect of Ang-(1-7) on Transforming growth factor-β1(TGF-β1)-induced EMT of human immortalized keratinocytes HaCaT in vitro. The study involved the use of the human immortalized keratinocyte cell line (HaCaT). The cells were cultured in high-glucose DMEM medium with 10% fetal bovine serum and 1% penicillin-streptomycin. Four groups were created for experimentation: control group (Group C), TGF-β1-treated group (Group T), Ang-(1-7)-treated group (Group A), and a group treated with both TGF-β1 and Ang-(1-7) (Group A + T). Various assays were conducted, including a cell proliferation assay using CCK-8 solution, a scratch wound healing assay to evaluate cell migration, and Western blotting to detect protein expressions related to cell characteristics. Additionally, quantitative real-time polymerase chain reaction (PCR) was performed to analyze epithelial-mesenchymal transition (EMT) related gene expression levels. The study aimed to investigate the effects of TGF-β1 and Ang-(1-7) on HaCaT cells. We found that Ang-(1-7) not only reduced the migration of HaCaT cells induced by TGF-β1 in vitro but also reduced the expression of α-SMA and vimentin, and restored the protein expression of E-cadherin and claudin-1. Mechanistically, Ang-(1-7) inhibits the phosphorylation levels of Smad2 and Smad3 in the TGF-β1 canonical pathway, and suppresses the expression of EMT-related transcription factors (EMT-TFs) such as SNAI2, TWIST1, and ZEB1. Taken together, our findings suggest that Ang-(1-7) inhibits TGF-β1-induced EMT in HaCaT cells in vitro by disrupting the TGF-β1-Smad canonical signaling pathway. These results may be helpful in the treatment of EMT in skin fibrotic diseases such as keloids.

Effect of human H3N2 influenza virus reassortment on influenza incidence and severity during the 2017–18 influenza season in the USA: a retrospective observational genomic analysis

During the 2017-18 influenza season in the USA, there was a high incidence of influenza illness and mortality. However, no apparent antigenic change was identified in the dominant H3N2 viruses, and the severity of the season could not be solely attributed to a vaccine mismatch. We aimed to investigate whether the altered virus properties resulting from gene reassortment were underlying causes of the increased case number and disease severity associated with the 2017-18 influenza season. Samples included were collected from patients with influenza who were prospectively recruited during the 2016-17 and 2017-18 influenza seasons at the Johns Hopkins Hospital Emergency Departments in Baltimore, MD, USA, as well as from archived samples from Johns Hopkins Health System sites. Among 647 recruited patients with influenza A virus infection, 411 patients with whole-genome sequences were available in the Johns Hopkins Center of Excellence for Influenza Research and Surveillance network during the 2016-17 and 2017-18 seasons. Phylogenetic trees were constructed based on viral whole-genome sequences. Representative viral isolates of the two seasons were characterised in immortalised cell lines and human nasal epithelial cell cultures, and patients' demographic data and clinical outcomes were analysed. Unique H3N2 reassortment events were observed, resulting in two predominant strains in the 2017-18 season: HA clade 3C.2a2 and clade 3C.3a, which had novel gene segment constellations containing gene segments from HA clade 3C.2a1 viruses. The reassortant re3C.2a2 viruses replicated with faster kinetics and to a higher peak titre compared with the parental 3C.2a2 and 3C.2a1 viruses (48 h vs 72 h). Furthermore, patients infected with reassortant 3C.2a2 viruses had higher Influenza Severity Scores than patients infected with the parental 3C.2a2 viruses (median 3·00 [IQR 1·00-4·00] vs 1·50 [1·00-2·00]; p=0·018). Our findings suggest that the increased severity of the 2017-18 influenza season was due in part to twointrasubtypes, cocirculating H3N2 reassortant viruses with fitness advantages over the parental viruses. This information could help inform future vaccine development and public health policies. The Center of Excellence for Influenza Research and Response in the US, National Science and Technology Council, and Chang Gung Memorial Hospital in Taiwan.

Establishment and characterization of a golden pompano (Trachinotus blochii) fin cell line for applications in marine fish pathogen immunology

Pompano fishes have been widely farmed worldwide. As a representative commercial marine species of the Carangidae family, the golden pompano (Trachinotus blochii) has gained significant popularity in China and worldwide. However, because of rapid growth and high-density aquaculture, the golden pompano has become seriously threatened by various diseases. Cell lines are the most cost-effective resource for in vitro studies and are widely used for physiological and pathological research owing to their accessibility and convenience. In this study, we established a novel immortal cell line, GPF (Golden pompano fin cells). GPF has been passaged over 69 generations for 10 months. The morphology, adhesion and extension processes of GPF were evaluated using light and electron microscopy. GPF cells were passaged every 3 days with L-15 containing 20 % fetal bovine serum (FBS) at 1:3. The optimum conditions for GPF growth were 28 °C and a 20 % FBS concentration. DNA sequencing of 18S rRNA and mitochondrial 16S rRNA confirmed that GPF was derived from the golden pompano. Chromosomal analysis revealed that the number pattern of GPF was 48 chromosomes. Transfection experiments demonstrated that GPF could be utilized to express foreign genes. Furthermore, heavy metals (Cd, Cu, and Fe) exhibited dose-dependent cytotoxicity against GPF. After polyinosinic-polycytidylic acid (poly I:C) treatment, transcription of the retinoic acid-inducible gene I-like receptor (RLR) pathway genes, including mda5, mita, tbk1, irf3, and irf7 increased, inducing the expression of interferon (IFN) and anti-viral proteins in GPF cells. In addition, lipopolysaccharide (LPS) stimulation up-regulated the expression of inflammation-related factors, including myd88, irak1, nfκb, il1β, il6, and cxcl10 expression. To the best of our knowledge, this is the first study on the immune response signaling pathways of the golden pompano using an established fin cell line. In this study, we describe a preliminary investigation of the GPF cell line immune response to poly I:C and LPS, and provide a more rapid and efficient experimental material for research on marine fish immunology.

A Review of the Repair of DNA Double Strand Breaks in the Development of Oral Cancer.

We explore the possibility that defects in genes associated with the response and repair of DNA double strand breaks predispose oral potentially malignant disorders (OPMD) to undergo malignant transformation to oral squamous cell carcinoma (OSCC). Defects in the homologous recombination/Fanconi anemia (HR/FA), but not in the non-homologous end joining, causes the DNA repair pathway to appear to be consistent with features of familial conditions that are predisposed to OSCC (FA, Bloom's syndrome, Ataxia Telangiectasia); this is true for OSCC that occurs in young patients, sometimes with little/no exposure to classical risk factors. Even in Dyskeratosis Congenita, a disorder of the telomerase complex that is also predisposed to OSCC, attempts at maintaining telomere length involve a pathway with shared HR genes. Defects in the HR/FA pathway therefore appear to be pivotal in conditions that are predisposed to OSCC. There is also some evidence that abnormalities in the HR/FA pathway are associated with malignant transformation of sporadic cases OPMD and OSCC. We provide data showing overexpression of HR/FA genes in a cell-cycle-dependent manner in a series of OPMD-derived immortal keratinocyte cell lines compared to their mortal counterparts. The observations in this study argue strongly for an important role of the HA/FA DNA repair pathway in the development of OSCC.

Abstract NG03: Functional and computational approaches to uncover selection advantages of cancer aneuploidy

Abstract Aneuploidy, including the gain or loss of whole chromosomes or chromosome arms, is a near-universal feature of cancer. We previously applied methods that define chromosome arm aneuploidy to over 10,000 tumors in the Cancer Genome Atlas (TCGA). Cancer subtypes are often characterized by tumor specific patterns of chromosome arm copy number alterations and breakpoints; for example, squamous cell carcinomas (SCCs) from different tissues of origin are characterized by chromosome 3p (chr3p) loss and chromosome 3q (chr3q) gain. From the TCGA aneuploidy data, we developed an algorithm called BISCUT to distinguish peak regions of aneuploidy breakpoints on each chromosome arm. BISCUT identified loci affected by broad copy number alterations that provide fitness advantages or disadvantages both within individual cancer types and across cancers. Our analyses are consistent with selection being the primary driver of aneuploidy events in cancer. We next wanted to validate some BISCUT peaks without a known driver, to identify potential gene deletions that are beneficial in cancer cells. We focused on chromosome 8p (chr8p), as this arm is frequently deleted across cancer types, but no strong tumor suppressors have been identified. Recent advances in genome engineering allow generation of large chromosomal alterations and validation of findings from patient genomic data. For this study, we used our CRISPR-Cas9 arm-deletion system to delete chr8p in human immortalized epithelial cells. Cells with chr8p deletion showed lower amounts of cell death in culture. Knockdown of WRN, one of the two genes in the smallest chr8p BISCUT peak, was sufficient to reproduce this phenotype, suggesting that WRN haploinsufficiency may be beneficial to tumor development. As aneuploidy occurs in tissue-specific patterns, we also wanted to explore the role of chr3 arm aneuploidies in squamous cancers. We again used the CRISPR-Cas9 system to delete one copy of chr3p in a human immortalized lung epithelial cell line similar to the putative cell-of-origin in lung SCC. Consistent with patient data, expression of chr3p genes was decreased upon deletion, as well as increased expression of interferon response genes. Cells with chr3p deletion initially proliferated more slowly than their siblings. Interestingly, after several passages in culture, this proliferation defect was rescued in chr3p deleted cells. Genome sequencing and karyotype analyses suggested that this was partially the result of chr3 duplication, with cells transitioning to a state of chr3q gain. Culturing these cells as organoids also demonstrated that chr3p deletion and chr3q gain can affect basal cell differentiation, consistent with their high frequency in squamous cancers. Our genome engineering approach to model chromosome arm aneuploidies provides a robust model to validate drivers from aneuploidy events, which will be critical to address the gap in our understanding of aneuploidy in cancer. In addition, our methods have identified consequences of individual aneuploidy events, which will lead to new precision oncology targets for patients. Citation Format: Alison M. Taylor. Functional and computational approaches to uncover selection advantages of cancer aneuploidy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr NG03.

CRL4DCAF4 E3 ligase-mediated degradation of MEN1 transcriptionally reactivates hTERT to sustain immortalization in colorectal cancer cells.

Telomerase reactivation is implicated in approximately 85% of human cancers, yet its underlying mechanism remains elusive. In this study, we elucidate that the Cullin RING Ubiquitin Ligase 4 (CRL4) complex drives the reactivation of human telomerase reverse transcriptase (hTERT) in colorectal cancer (CRC) by degrading the tumor suppressor, menin 1 (MEN1). Our data show that, in noncancerous intestinal epithelial cells, the transcription factor specificity protein 1 (Sp1) recruits both the histone acetyltransferase p300 and MEN1 to suppress hTERT expression, thus maintaining telomere shortness post-cell division. Inflammation-induced microenvironments trigger an activation of the CRL4DCAF4 E3 ligase, leading to MEN1 ubiquitination and degradation in CRC cells. This process nullifies MEN1's inhibitory action, reactivates hTERT expression at the transcriptional level, interrupts telomere shortening, and spurs uncontrolled cellular proliferation. Notably, MEN1 overexpression in CRC cells partially counteracts these oncogenic phenotypes. NSC1517, an inhibitor of the CRL4DCAF4 complex identified through high-throughput screening from a plant-derived chemical pool, hinders MEN1 degradation, attenuates hTERT expression, and suppresses tumor growth in mouse xenograft models. Collectively, our research elucidates the transcriptional mechanism driving hTERT reactivation in CRC. Targeting the CRL4DCAF4 E3 ligase emerges as a promising strategy to counteract cancer cell immortalization and curb tumor progression.

Omenn Syndrome in Two Infants with Different Hypomorphic Variants in Janus Kinase 3.

Biallelic null or hypomorphic variants in JAK3 cause SCID and less frequently Omenn syndrome. We investigated homozygous hypomorphic JAK3 mutations in two patients, and expression and function of a novel JAK3R431P variant in Omenn syndrome. Immunophenotyping of PBMC from the patient with the novel JAK3R431P variant was undertaken, by flow cytometry and Phosflow after stimulation with IL-2, IL-7, and IL-15. JAK3 expression was investigated by Western blotting. We report two patients with homozygous hypomorphic JAK3 variants and clinical features of Omenn syndrome. One patient had a previously described JAK3R775H variant, and the second had a novel JAK3R431P variant. One patient with a novel JAK3R431P variant had normal expression of JAK3 in immortalised EBV-LCL cells but reduced phosphorylation of STAT5 after stimulation with IL-2, IL-7, and IL-15 consistent with impaired kinase activity. These results suggest the JAK3R431P variant to be hypomorphic. Both patients are alive and well after allogeneic haematopoietic stem cell transplantation. They have full donor chimerism, restitution of thymopoiesis and development of appropriate antibody responses following vaccination. We expand the phenotype of hypomorphic JAK3 deficiency and demonstrate the importance of functional testing of novel variants in disease-causing genes.

Fructose-1,6-bisphosphatase 1 dephosphorylates and inhibits TERT for tumor suppression.

Telomere dysfunction is intricately linked to the aging process and stands out as a prominent cancer hallmark. Here we demonstrate that telomerase activity is differentially regulated in cancer and normal cells depending on the expression status of fructose-1,6-bisphosphatase 1 (FBP1). In FBP1-expressing cells, FBP1 directly interacts with and dephosphorylates telomerase reverse transcriptase (TERT) at Ser227. Dephosphorylated TERT fails to translocate into the nucleus, leading to the inhibition of telomerase activity, reduction in telomere lengths, enhanced senescence and suppressed tumor cell proliferation and growth in mice. Lipid nanoparticle-mediated delivery of FBP1 mRNA inhibits liver tumor growth. Additionally, FBP1 expression levels inversely correlate with TERT pSer227 levels in renal and hepatocellular carcinoma specimens and with poor prognosis of the patients. These findings demonstrate that FBP1 governs cell immortality through its protein phosphatase activity and uncover a unique telomerase regulation in tumor cells attributed to the downregulation or deficiency of FBP1 expression.

Abstract 4652: Combined inhibition of MCL-1 and MEK reduces tumor growth in a triple-negative/inflammatory breast cancer, MEK-resistant xenograft mouse model

Abstract Background: Triple-negative breast cancer (TNBC) and inflammatory breast cancer (IBC) are highly aggressive subtypes of invasive breast cancer. Our previous work showed that the MEK inhibitor (MEKi) selumetinib (AZD6244) prevents lung metastasis in a xenograft model. However, clinical studies have shown that MEKi’s as single agents have only modest activity against solid tumors. Using a genome-wide synthetic lethal siRNA screening, we identified myeloid cell leukemia-1 (MCL1) as a potential contributor to selumetinib resistance. MCL-1 is an anti-apoptotic protein associated with cell immortalization, transformation, and chemoresistance in numerous cancers. We hypothesized that MCL-1 promotes MEKi resistance in TNBC/IBC and inhibition of MCL-1 in the presence of AZD6244 overcomes this MEKi resistance. Methods & Results: To understand MCL1’s role in MEKi resistance, we established two AZD6244 -resistant TNBC/IBC cell lines: MDA-MB-231-R and SUM149-R. These cells showed increased cell viability, colony formation, migration, cells in G1 phase, CD44+CD24low, mammosphere count, anchorage-independent growth and high MCL-1 expression. MCL-1’s biological role was evaluated by transient and stably knock down (KD) of MCL-1 in the resistant cells which showed decreased cell viability, colony formation, and increased apoptosis. To understand the mechanism mediating apoptosis, we examined the expression of MCL-1’s binding partners in the MCL-1-KD-R cells in the presence of AZD6244. These cells showed a high expression of the PUMA, NOXA, BAK, and BAX in the presence of AZD6244. Further, we treated resistant cells with MEKi AZD6244 and an MCL-1i (AZD5991) that confirmed restoration of MEK sensitivity in both resistant cell lines, resulting in decreased cell viability, colony formation and increased apoptosis. We compared tumor formation capability between SUM149 parental and SUM149 resistant cells by injecting them in nu/nu mice and observed a time-dependent increase (avg. 4-fold) in tumor growth with SUM149-R cells compared to parental cells (P≤0.0001). Moreover, IHC analysis showed high expression of MCL-1 (P≤0.01), Ki67 (ns), CD44 (P≤0.0001), and ALDHA1 (P≤0.0001) in the mammary gland tumor tissues of SUM149-R-injected mice compared to SUM149-P-injected mice. Next, we evaluated the therapeutic effect of AZD6244 in mice harboring SUM149-R - MCL-1-deficient tumors. AZD6244 treatment significantly reduced tumor development in mice harboring SUM149-R - MCL-1-KD tumors compared to control mice (P<0.0001), suggesting that MCL-1 mediates MEK resistance in triple-negative/inflammatory breast cancer. Conclusion: Our results suggest that MCL-1 is important for inducing acquired MEK resistance and combining an MCL-1i with a MEKi could improve treatment outcomes of patients with TNBC or IBC who have developed resistance to single-agent MEKi. Citation Format: Mohd Mughees, Alex Tan, Lakesla Iles, Michael White, Debu Tripathy, Savitri Krishnamurthy, Jian Wang, Wendy A. Woodward, Geoffrey Bartholomeusz, Chandra Bartholomeusz. Combined inhibition of MCL-1 and MEK reduces tumor growth in a triple-negative/inflammatory breast cancer, MEK-resistant xenograft mouse model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4652.

Abstract 336: Genome integrity assessment by optical genome mapping for cell manufacturing/bioprocessing applications

Abstract Cells and cell lines are used for multiple applications such as bioprocessing, therapy, and research. To ensure quality of cells and downstream applications, appropriate quality control (QC) methods are critical. Historically, karyotyping has been employed, but it is limited by its very low resolution and tedious laboratory workflow. Other methods such as PCR and targeted sequencing can characterize only small genomic variants at specific loci. Whole genome sequencing can detect small variants genome-wide but has limited sensitivity in detecting structural variants (SVs). Optical genome mapping (OGM) is a novel genome analysis technique that can fill many of the gaps in current capabilities for assessing genome integrity. To find clonal variants, 400 Gbp of data is collected from the parental/control and test samples. For both samples, a de novo assembly is constructed, and homozygous or heterozygous SVs are assessed. Subsequently, the dual variant annotation pipeline identifies unique SVs in the test sample compared to the parental sample. To discover subclonal SVs down to 5% variant allele fraction (VAF), the workflow leverages the generation of 1.5 Tbp of data, requiring a simple adjustment to longer data collection time. Comparison of test sample to parental sample enables easy determination of acquired variants. Finally, generation of ~5 Tbp of data, requiring 2-3 flowcells to be run, enables the detection of SVs at ultra-low VAF down to ~1%. In this study, several dilutions and simulations were performed to examine OGM’s limit of detection. Targeting a coverage of 5 Tbp and analysis using the somatic SV-analysis workflow revealed that OGM has the sensitivity to detect deletions >50kbp, insertions >20kbp, duplications >100 kbp, and translocations at ~1% VAF. We have applied the clonal and somatic workflows to verify genomes’ integrity after cell immortalization, induced pluripotency, transgene-integration, and gene-editing. The data using the robust and sensitive workflows demonstrate that the OGM platform is a cost-effective solution for cell manufacturing/bioprocessing QC applications. Citation Format: Alex Hastie, Andy W. Pang, Alka Chaubey. Genome integrity assessment by optical genome mapping for cell manufacturing/bioprocessing applications [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 336.

Abstract 1874: Common vulnerabilities of stem cells along the Barrett's-dysplasia-adenocarcinoma sequence

Abstract Barrett's esophagus (BE) is an early precursor of esophageal adenocarcinoma and therefore a relevant target of preemptive therapeutics. Using robust stem cell cloning technologies, we have cloned stem cells from patient-matched biopsies of BE, low-grade dysplasia (LGD), high-grade dysplasia (HGD), and esophageal adenocarcinoma (EAC) from multiple patients. Whole exome sequencing of these stem cells reveals the mutational maturation along the sequence of BE, LGD, HGD, and EAC at unprecedented resolution of both copy number and single nucleotide variation. In vitro differentiation and xenografting of these clones recapitulates their original histology and shows that only the EAC stem cells yield robust tumors in immunodeficient mice. Leveraging the intrinsic immortality of these stem cells, we have performed high-throughput screens for small molecules that selectively kill BE stem cells without harming patient-matched normal esophageal stem cells. These screening efforts evolved into synthetic lethal strategies that identified drug combinations that selectively eliminate, in vitro, BE stem cells from 20 of 23 cases. Remarkably, this same synthetic lethal drug combination also eliminated in vitro stem cells of LGD, HGD, and EAC that were not components of the original screens. We have used synthetic chemistry to generate a series of novel molecules based on the identified drug combination that significantly improved the in vitro efficacy to sub-nanomolar levels. These novel molecules directed to the stem cell component of BE, LGD, HGD, and EAC also show potent effects against tumors generated from EAC stem cells in immunodeficient mice. We anticipate that these synthetically lethal drug combinations will have potential utility against precursor lesions to preempt EAC as well as against EAC itself. Citation Format: Wa Xian, Frank McKeon, Christopher Crum, Jaffer Ajani, Peter Davies, Matthew Vincent, William Bachovchin, Hung-Sen Lai, Shuang Pan, Amber Su, Ashley Hoffman, Raul Caballero Montes, Melina Khorrami, Melika Khorrami, Yusuke Yamamoto. Common vulnerabilities of stem cells along the Barrett's-dysplasia-adenocarcinoma sequence [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1874.

Abstract 4551: A novel MET antibody-drug conjugate based combination therapy to overcome colorectal cancer plasticity and drug resistance

Abstract Despite therapeutic advancements, colorectal cancer (CRC) remains the second deadliest malignancy in the United States. Challenges encountered in CRC treatment may be attributed to cancer stem cells (CSC), an immortal tumor cell population. CSCs potentiate tumor relapse by exploiting its infinite replicative potential and inherent drug resistance. Moreover, CSCs exhibit plasticity, allowing them to transition between differentiated and undifferentiated states in response to environmental cues to evade therapy and drive metastatic progression. MET is a receptor tyrosine kinase frequently upregulated in CRCs. We previously demonstrated that treatment with chemotherapies or antibody-drug conjugates (ADCs) targeting the CSC marker LGR5 led to the loss of LGR5 expression with concomitant MET-STAT3 pathway activation in therapy-resistant CRC cells. Further, we showed that LGR5 couples to the scaffold protein IQGAP1, which correlates with poor prognosis in several cancer types. Interestingly, our new data revealed that LGR5 knockdown enhances IQGAP1 interaction with MET and STAT3 via co-immunoprecipitation assays, suggesting a role for IQGAP1 in mediating MET-STAT3 activation and plasticity of LGR5+ CRC cells. To overcome therapy-induced plasticity, we generated MET-targeting ADCs conjugated to DNA-crosslinking payloads. First, we cloned and produced MET monoclonal antibodies (mAbs) and evaluated them for specificity and binding in a panel of CRC cell lines expressing different MET protein levels. MET mAbs demonstrated high selectivity for MET-expressing CRC cells and internalized to lysosomes, which is necessary for ADC payload release. To generate MET ADCs, we employed a site-specific conjugation methodology to attach cleavable peptide linker-drug moieties to the highest affinity MET mAb. MET ADCs were evaluated for cancer cell-killing efficacy in vitro in parallel with MET mAb, non-targeting control mAb (cmAb), and control ADC (cADC). Our MET ADC displayed high potency and efficacy in MET-expressing CRC cells, whereas MET mAb, cmAb, and cADC had minimal effects. MET ADCs were then tested in combination with chemotherapies or other targeted therapies. The combination of MET ADCs with 5-fluorouracil showed a synergistic effect in vitro. Future work involves investigating the safety and efficacy of MET ADCs alone and combined with chemotherapies in xenograft models of CRC. These findings present a mechanism underpinning CRC plasticity and the rationale for a novel treatment modality to potentially overcome CRC resistance and relapse. Citation Format: Shraddha Subramanian, Tressie A. Posey, Joan Jacob, Adela Aldana, Kendra S. Carmon. A novel MET antibody-drug conjugate based combination therapy to overcome colorectal cancer plasticity and drug resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 4551.

Abstract 1455: In vitro blood brain barrier model for evaluation of brain metastasis

Abstract Introduction: Brain metastasis significantly reduces the patient's quality of life and survival, but there are only a few choices of treatment for brain metastasis. The research for brain metastasis is difficult because of its complex and unique microenvironment, including blood-brain barrier (BBB). The BBB maintains strong cell adhesion of the vascular endothelial cells (ECs) to protect the brain parenchyma. The BBB is composed of three cell types: vascular endothelial cells, pericytes, and astrocytes. As the role of pericytes in maintaining the BBB function has become more evident, the reconstituted models of the BBB in which ECs, pericytes, and astrocytes are seeded on the front and back of the insert membrane have gotten our attention. In the field of cancer, the role of not only ECs but also wall cells, corresponding to pericytes in the brain, has been focused on. In this study, we aimed to create the in vitro BBB models and elucidate the interaction of the BBB and the metastasizing cancer cells. Methods: We applied a reconstituted model of the BBB consisting of ECs, pericytes, and astrocytes of human immortalized cells (Ito R, et al. Mol Pharm 2019) and created the co-culture system for evaluating brain metastasis. We constructed four co-culture systems and compared the migration ability of MDA231 in those models: EPA model (ECs, pericytes, and astrocytes), E0A model (ECs and astrocytes), EP0 model (ECs and pericytes), and E00 model (ECs only). We also analyzed the migration ability of the pairs of parental and brain metastatic (BrM) cell lines. Results: The BBB reconstituted model (EPA model), in which ECs were co-cultured with pericytes and astrocytes, showed higher trans-epithelial electrical resistance and lower permeability than the other co-culture models. When cancer cells were seeded, the EPA model strongly inhibited metastatic invasion of cancer cells compared to the other models. It suggests that both pericytes and astrocytes are essential for regulating cancer cell invasion. In addition, when the BrM cells of MDA231 and Ex3LL were seeded, the BrM cells invaded the EPA model more easily than the parental cells. It indicates that this model can reproduce in vivo brain vascular functions. Conclusion: We created the BBB reconstituted model which mimics the brain vascular microenvironment. This model reproduced the in vivo BBB function to protect brain from cancer cells and evaluated the brain metastatic ability of the cancer cells. Using this model, we showed that pericytes and astrocytes were essential for the BBB barrier function against the cancer cells. We need further investigation to elucidate the mechanism of brain metastasis using this BBB model. Citation Format: Shoko Noda-Narita, Atsu Aiba. In vitro blood brain barrier model for evaluation of brain metastasis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1455.

Abstract 2791: Establishment of immortalized endometrial cell lines using Sendai virus

Abstract Objective: To establish endometrial immortalized cell lines using the Sendai virus and analyze their characteristics. Methods: The study included patients with benign ovarian tumors and endometrioid carcinoma who had regular menstrual cycles. Endometrial cells were collected and separated into epithelial and non-epithelial cells using flowcytometry (FCM) (CD326 (EpCAM) antibody). Furthermore, the isolated cells were infected with Sendai virus carrying three immortalization genes (Bmi-1, hTERT, and SV40T) to create immortalized cell lines. The cells were characterized as epithelial cells by immunocytochemistry (ICC), and receptor expression was assessed by reverse transcription PCR (RT-PCR) and ICC. Non-epithelial cells from the patients with endometrial carcinoma were evaluated using ICC. Results: The immortalized cell lines were capable of more than 20 passages. Immortalized endometrial epithelial cells tested positive for anti-Keratin antibodies and negative for anti-Vimentin antibodies by ICC. Additionally, FCM detected these cells as positive for anti-EpCAM antibody, confirming that they were epithelial cells. RT-PCR confirmed mRNA expression of estrogen α-receptor and progesterone receptor after 20 passages and ICC confirmed protein expression of them after 10 passages, establishing an endometrial epithelial immortalized cell line. Non-epithelial cells isolated from patients with endometrial carcinoma tested positive for anti-α-smooth muscle actin and anti-Vimentin antibodies by ICC, indicating their characterization as cancer-associated fibroblasts. Conclusion: We successfully established an immortalized cell line of endometrial epithelial cells using Sendai virus and generated cancer-associated fibroblasts. Citation Format: Kohei Hikino, Hiroaki Komatsu, Genki Hichiwa, Kanako Kazuki, Yasuhiro Kazuki, Hiroyuki Kugoh, Masayo Okawa, Yuki Ida, Masayo Hosokawa, Mayumi Sawada, Akiko Kudoh, Shinya Sato, Fuminori Taniguchi. Establishment of immortalized endometrial cell lines using Sendai virus [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2791.

Abstract 2995: The ectopic expression of miR-380-5p interferes with the aggressive traits of diffuse malignant peritoneal mesothelima cells

Abstract Telomerase activity (TA) and the alternative lengthening of telomere (ALT) pathway are two telomere maintenance mechanisms (TMM) yet identified in human cancers. Although the activation of either TMM seems to be equivalent in supporting tumor cell immortalization (a hallmark of cancer), the contribution of TA and ALT to tumor progression and aggressiveness may be different. Mounting evidence suggests that cancer cell aggressiveness could be associated with a TA↔ALT shift that would allow the acquisition of distinct aggressive traits. We previously showed that an ALT-like phenotype emerged in diffuse malignant peritoneal mesothelioma (DMPM) cells upon miR-380-5p-dependent inhibition of TA (Cimino-Reale G, et al. J Hematol Oncol. 2017). To analyze the transcriptomic changes associated with the emergence of such a phenotype, gene expression profiling was carried out. Results showed that 3331 genes were differentially expressed (FDR<0.05, adjusted for multiple hypothesis testing) in miR-380-5p- vs. preNeg-transfected DMPM cells, out of which 1673 genes were up-regulated and 1658 genes down-regulated. To get biological meaning about the molecular events occurring upon miR-380-5p reconstitution, Gene Set Enrichment Analysis was performed. Results showed a positive enrichment of 188 gene sets, restricted for an FDR < 0.05, out of which signatures related to DNA replication, DNA recombination and telomere maintenance via recombination were present. Conversely, only 1 gene set (GO: positive regulation of blood vessel endothelial cell migration) was negatively enriched at significant level. Notably, among the leading edge genes, PTGS2, which encodes for cyclooxygenase-2 (COX-2) and represents a predicted target of miR-380-5p (miRWalk), was the most significantly down-regulated gene (FDR< 0.000001; log(fold-change): -2.15). Notably, a complete abrogation of PTGS2 expression levels and COX-2 protein amounts was observed in miR-380-5p- compared to preNeg-transfected cells upon validation by qRT-PCR and western blotting, respectively. This evidence was paralleled by reduced amounts of phospho-FAK (focal adhesion kinase) and impaired migrating/invading capabilities of cells ectopically expressing miR-380-5p. Moreover, a reduction of Vimentin and a slight increase in P-Cadherin protein levels were also observed in cells ectopically expressing miR-380-5p, likely indicating the occurrence of a reverse-EMT program. Finally, a pronounced increase in the sensitivity to Cisplatin and Doxorubicin was also appreciable in miR-380-5p- vs. preNeg-transfected cells, suggesting that miRNA-mediated induction of a reverse-EMT may, at least in part, contribute to improve the response of DMPM cells to chemotherapeutic drugs. Citation Format: Stefano Percio, Lorenzo Di Pietro, Eisa Naghshineh, Marcello Deraco, Nadia Zaffaroni, Marco Folini. The ectopic expression of miR-380-5p interferes with the aggressive traits of diffuse malignant peritoneal mesothelima cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2995.

Cell Immortality: In Vitro Effective Techniques to Achieve and Investigate Its Applications and Challenges.

Cells are very important to researchers due to their use in various biological studies in in vitro and in vivo settings. This importance stems from the short lifespan of most cells under laboratory conditions, which can pose significant challenges, such as the difficulties associated with extraction from the source tissue, ethical concerns about separating cells from human or animal models, limited cell passage ability, and variation in results due to differences in the source of the obtained cells, among other issues. In general, cells in laboratory conditions can divide into a limited number, known as the Hayflick limit, due to telomere erosion at the end of each cellular cycle. Given this problem, researchers require cell lines that do not enter the senescence phase after a limited number of divisions. This can allow for more stable studies over time, prevent the laborious work associated with cell separation and repeated cultivation, and save time and money in research projects. The aim of this review is to summarize the function and effect of immortalization techniques, various methods, their advantages and disadvantages, and ultimately the application of immortalization and cell line production in various research fields.

Mechanisms underlying morphological and functional changes of cilia in fibroblasts derived from patients bearing ARL3T31A and ARL3T31A/C118F mutations.

ARL3 is essential for cilia development, and mutations in ARL3 are closely associated with ciliopathies. In a previous study, we observed distinct phenotypes of retinal dystrophy in patients with heterozygous ARL3T31A and compound heterozygous ARL3T31A/C118F mutations, indicating that different mutation types may exert diverse effects on their functions. Here, we generated transformed immortal fibroblast cells from patients carrying heterozygous ARL3T31A and compound heterozygous ARL3T31A/C118F mutations, and systematically evaluated their cilia morphology and function, which were further validated in ARPE-19 cells. Results showed that both ARL3T31A and ARL3T31A/C118F mutations led to a decrease in cilium formation. The ARL3T31A/C118F mutations caused significantly elongated cilia and impaired retrograde transport, whereas the ARL3T31A mutation did not induce significant changes in fibroblasts. RNA-sequencing results indicated that compared to ARL3T31A , ARL3T31A/C118F fibroblasts exhibited a higher enrichment of biological processes related to neuron projection development, tissue morphogenesis, and extracellular matrix (ECM) organization, with noticeable alterations in pathways such as ECM-receptor interaction, focal adhesion, and TGF-β signaling. Similar changes were observed in the proteomic results in ARPE-19 cells. Core regulated genes including IQUB, UNC13D, RAB3IP, and GRIP1 were specifically downregulated in the ARL3T31A/C118F group, and expressions of IQUB, NPM2, and SLC38A4 were further validated. Additionally, IQUB showed a rescuing effect on the overlong cilia observed in ARL3T31A/C118F fibroblasts. Our results not only enhance our understanding of ARL3-related diseases but also provide new insights into the analysis of heterozygous and compound heterozygous mutations in genetics.

A metabolic map and artificial intelligence-aided identification of nasopharyngeal carcinoma via a single-cell Raman platform.

Nasopharyngeal carcinoma (NPC) is a complex cancer influenced by various factors. This study explores the use of single-cell Raman spectroscopy as a potential diagnostic tool for investigating biomolecular changes associated with NPC carcinogenesis. Seven NPC cell lines, one immortalised nasopharyngeal epithelial cell line, six nasopharyngeal mucosa tissues and seven NPC tissue samples were analysed by performing confocal Raman spectroscopic measurements and imaging. The single-cell Raman spectral dataset was used to quantify relevant biomolecules and build machine learning classification models. Metabolomic profiles were investigated using ultra-performance liquid chromatography-tandem mass spectrometer (UPLC-MS/MS). By generating a metabolic map of seven NPC cell lines, we identified an interplay of altered metabolic processes involving nucleic acids, amino acids, lipids and sugars. The results from spatially resolved Raman maps and UPLC-MS/MS metabolomics were consistent, revealing an increase of unsaturated fatty acids in cancer cells, particularly in highly metastatic 5-8F and poorly differentiated CNE2 cells. The classification model achieved a nearly perfect classification when identifying NPC and non-NPC cells with an ROC-AUC of 0.99 and a value of 0.97 when identifying 13 tissue samples. This study unveils a complex interplay of metabolic network and highlights the potential roles of unsaturated fatty acids in NPC progression and metastasis. This renders further research to provide deeper insights into NPC pathogenesis, identify new metabolic targets and improve the efficacy of targeted therapies in NPC. Artificial intelligence-aided analysis of single-cell Raman spectra has achieved high accuracies in the classification of both cancer cells and patient tissues, paving the way for a simple, less invasive and accurate diagnostic test.