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15 protocols using hcc2218

1

Cell Line Maintenance and Reagents

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AU565, HCC1419, NCI-H2170, HCC202, HCC1954, NCI-N87, ZR75-1, SKOV3, ZR75-30, MDAMB175VII, CALU3, MDAMB453, MDAMB361, JIMT1, SKBR3 and HCC2218 cells were obtained from ATCC. OE19 and OE33 were obtained from ECCC; COLO-678 was obtained from DSMZ, and KYSE-410 from Sigma-Aldrich. BT-474-M3 cells (hereafter simply referred to as BT-474) were obtained from Hermes biosciences. All cell lines were maintained in RPMI supplemented with 10% FBS, penicillin, and streptomycin. GSK-1120212 and MK-2206 were purchased from Selleckchem. Recombinant human HRG-β1 (EGF domain) was from R&D Systems.
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2

Culturing Breast Cancer Cell Lines

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MDA-MB-453, UACC-893, HCC-2218, HCC-1419 (ATCC, Manassas, VA, USA), and ZR-75-1 cells (Institute of Development, Aging and Cancer (IDAC), Miyagi, Japan) were cultured in Roswell Park Memorial Institute medium (RPMI-1640, FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan) supplemented with 10% heat-inactivated fetal bovine serum (FBS, NICHIREI BIOSCIENCES INC., Tokyo, Japan), 100 U/mL penicillin (Meiji-Seika Pharma Co., Ltd., Tokyo, Japan), and 100 µg/mL streptomycin (Meiji-Seika Pharma) at 37 °C with 5% CO2. MDA-MB-361 and HCC-202 cells (ATCC) were cultured in RPMI-1640 (FUJIFILM Wako Pure Chemical Corporation) supplemented with 15% heat-inactivated FBS, 100 U/mL penicillin (Meiji Seika Pharma), and 100 µg/mL streptomycin (Meiji-Seika Pharma) at 37°C with 5% CO2. BT-474, UACC-812, and 293T cells (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (DMEM, FUJIFILM Wako Pure Chemical Corporation) supplemented with 10% heat-inactivated FBS, 100 U/mL penicillin (Meiji Seika Pharma), and 100 µg/mL streptomycin (Meiji-Seika Pharma) at 37 °C with 5% CO2. Luc2-expressing breast cancer cell lines were established by infection with lentivirus (pLenti-PEF1-luc2-IRES-BlaR) and selection by blasticidin (Kaken Pharmaceuticals Co. Ltd., Tokyo, Japan).
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3

CNA Detection Performance Evaluation

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For CNA detection performance, cell-line DNA from MCF7 (Lot #60540387), HCC2218 (Lot #64097142), and HCC827 (Lot #64216187; all obtained from ATCC) and the HapMap cell-line NA24143 were used following acoustic shearing to 200 bp on an ME220 Focused-ultrasonicator. The HCC827 cell-line harbors a 32.6-fold increase in EGFR copy number over the diploid number, as verified by the manufacturers via ddPCR. Fragmented HCC2218 DNA was mixed with fragmented NA24143 DNA to generate cell-line DNA admixtures containing EGFR copy numbers of 30, 20, 10, 4, 3, and 2.4. The HCC2218 cell-line harbors a 16.32-fold increase in ERBB2 (HER2) copy number [30 (link)], and the MCF7 cell-line harbors an estimated 4.46-fold increase in NRAS copy number, 3.34-fold increase in MYC copy number, and a 1.80-fold increase in CDK6 copy number [31 (link),32 (link)]. Fragmented MCF7 DNA was mixed with fragmented NA24143 DNA to generate cell-line DNA admixtures containing 4.3 copies of NRAS and 3.6 copies of MYC, and 3.2 copies of NRAS and 2.8 copies of MYC. The HD786 reference standard harbors focal MET and MYC amplification at 4.5 and 9.5 copies respectively.
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4

Characterization of Breast Cancer Cell Lines

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Cell lines were obtained from ATCC (HCC2218, HCC1954, HCC1419, ZR-75-30, AU565, NCI-2170, BT-474, SK-BR-3, NCI-N87, SKOV3, MCF7), Sigma (OE-19), DSMZ (JIMT-1), Cedarlane (ZR-75-1) and AddexBio (MDA-MB-175-VII, MDA-MB-468). Cell lines were authenticated by supplier and were used from source and expanded for a maximum of 20 passages. Cell lines were routinely spot check tested for mycoplasma, all tests were negative. Cell line supplier and catalog numbers are provided in Supplementary Table 14. Trastuzumab (Herceptin®) and pertuzumab (Perjeta®) were purchased from Crown Bio and Xentech, respectively. Zanidatamab was prepared according to standard manufacturing procedures (CMC Bio). A non-specific IgG1 Ab that binds to respiratory syncytial virus (RSV) protein F, palivizumab, was used as a negative control (neg. control or NC) and was produced under standard expression and purification conditions. Human complement serum, baby rabbit complement serum and pooled murine complement serum were obtained from Cedarlane. Mouse strain serum (male and female Balb/c, male and female CB17 SCID) was collected under protocols that were approved by the Animal Care Committee at University of British Columbia.
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5

Authenticated Cell Lines Maintenance

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The following cell lines were purchased from ATCC: AU565, BT474, Calu-3, HCC1419, HCC2218, H358, MCF7, N-87, SKBR3, UACC-893, and ZR-75-30. Cell lines CW-2 and MKN-7 were obtained from RIKEN Biobank, Japan. RIKEN Biobank is the authentic source for MKN-7, a commonly misidentified cell line. Hela cells for the single-molecule tracking experiments were provided by the laboratory of Prof. J. Piehler. Cell lines were maintained at 37 °C/5% CO2 in a humidified atmosphere and routinely checked for mycoplasma contamination.
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6

Transcriptomic Analysis of HER2+ Breast Tumors

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We retrospectively analyzed 45 frozen HER2+++ tumors (Table 1). In addition, we also studied 34 FFPE HER2+++ tumors (Table 1). The study was conducted in accordance with the Declaration of Helsinki and approved by an Ethics Committee, the Comité Consultatif de Protection des Personnes en Recherche Biomédicale de Bourgogne. Written informed consent was obtained from all patients before enrollment. RNA was extracted from frozen samples as described previously [4 (link)] and from FFPE samples with the RNeasy FFPE kit (Qiagen) by following manufacturer’s protocol.

Demographic data of patients analyzed

Clinical parametersFrozen samples n = 45FFPE samples n = 34
Age
≤502824
>501710
Hormone receptors
Estrogen Receptors -1815
Estrogen Receptors +2719
Progesterone Receptors -2417
Progesterone Receptors +2117
Grade
142
22319
31611
Not available22
Tumour size
2-4 cm2318
>4 cm75
Not available1511
Pathological response
pCR1812
non-pCR2722
Trastuzumab-sensitive cell lines BT474, HCC2218, UACC-812, and resistant cell lines HCC1419, HCC1954, and HCC1569 were obtained from ATCC and cultured in accordance with the supplier’s instructions. The treatment of cells before RNA extraction was identical to that for patients’ tumors.
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7

Cell Line Procurement and Maintenance

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BT474, HCC1954, SKOV3, HCC2218, AU565, Toledo, Raji, Jurkat, FaDu, NCI.H747, SW48, and Cal27 were purchased from ATCC in either 2020 or 2021. ATCC has confirmed the identity of human cell lines by (short tandem repeat analyses. Cells were cultured and maintained in media supplemented with 10% or 20% of FBS per ATCC's recommendation. Fresh stocks of cells were made on early passages and fresh culture of each line was started every 2–3 months for in vitro assays. Mycoplasma testing was performed on cancer cell lines on July 6, 2022. Primary macrophages were not assessed for Mycoplasma.
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8

Cell Line Culturing Protocol

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All cell lines used for characterization of the automated platform (LNCaPs (gift from Dr. Douglas McNeel, University of Wisconsin-Madison), HCC2218 (ATCC), PC3-MM2 (gift from Dr. C. Pettaway, MD Anderson Cancer Centre, TX, USA), 22RV1 (gift from Dr. Douglas McNeel)) were cultured in RPMI1640 media (#11875–093, Thermo Fisher Scientific) supplemented with 10% Fetal Bovine Serum (Gibco) and 1% Penicillin Streptomycin (Gibco). Cells were maintained under sterile conditions at 37° C in 5% CO2.
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9

Comprehensive Cancer Cell Line Profiling

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A549, BT-20, BT-474, BT-549, CAMA-1, DMS-53, DU4475, HCC38, HCC70, HCC202, HCC1143, HCC1187, HCC1395, HCC1569, HCC1806, HCC1937, HCC1954, HCC2218, HCT-116, Hs578T, Jeko-1, MCF-7, MDA-MB-134-VI, MDA-MB-157, MDA-MB-175-VII, MDA-MB-231, MDA-MB-361, MDA-MB-415, MDA-MB-436, MDA-MB-453, MDA-MB-468, MiaPaCa2, SK-BR-3, NCI-H441, SK-MEL-28, T-47D, U2OS, and ZR-75-1 were obtained from the American Type Culture Collection (ATCC) and cultured according to vendor recommendations. EFM-19 were obtained from the German Collection of Microorganisms and Cell Cultures (DSMZ) and SNU-886 were from the Korean Cell Line Bank (KCLB).
Abemaciclib, palbociclib, ribociclib, PIM447, BYL719, LY2090314, everolimus, DYRK1Bi AZ cpd 33 [32 (link)], dinaciclib, GSK2334470, abemaciclib metabolites M2 and M20 [28 (link)], and additional CDK4/6i (see Figure 2C [33 ],) were synthesized by Lilly Research Laboratories. AZD1208 (S7104) and additional palbociclib (S1579, see Supplementary Figure 1A) were purchased from Selleck Chemicals.
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10

Breast Cancer Cell Line Characterization

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Breast cancer cells line MCF10A, MCF-7, MDA-MB-468, BT-483 and HCC2218 were obtained from American Type Culture Collection (ATCC, Manassas, VA, USA). Upon thawing and passaging, cells were used until passage number 20. Mycoplasma testing was done every other month, using the MycoAlert following manufacturers protocol (Lonza, Cat# LT07-318). Non-tumorigenic breast epithelial cell MCF10A cultured in DMEM supplemented with 5% horse serum, 1% penicillin-streptomycin. MDA-MB-468 and MCF-7 were cultured in DMEM mixed with F12 (DMEM/F12; Welgene) supplemented with 10% FBS and 1% penicillin-streptomycin. BT-483 and HCC2218 cells were cultured in RPMI-1640 supplemented with 20% FBS, 1% penicillin-streptomycin. Where required cells were treated with 200 μM of Sulfo-N-succinimidyl oleate (SSO), 100 μM STAT3 inhibitor (S3I-201) (Santa Cruz), 60 nM ERK1/2 inhibitor (U0126) (Santa Cruz) and 20 μM BMS-309402 (Millipore).
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