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10 protocols using jimt 1

1

Cell Culture Conditions for Cancer Cell Lines

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JIMT-1 (AddexBio), JIMT-1(MDR1+) (generated in-house, see the protocol below), HCC1954 (ATCC), HCC1954-TDR (generated in-house, see the protocol below), SKBR-3 (ATCC), and THP-1 cells (ATCC) were cultured in RPMI1640 (Corning) supplemented with 10% EquaFETAL® (Atlas Biologicals), GlutaMAX® (2 mM, Gibco), sodium pyruvate (1 mM, Corning), and penicillin–streptomycin (penicillin: 100 units mL−1; streptomycin: 100 µg mL−1, Gibco). KPL-4 (provided by Dr. Junichi Kurebayashi at Kawasaki Medical School), MDA-MB-231 (ATCC), HepG2 (ATCC), and HEK293 (ATCC) were cultured in Dulbecco’s modified Eagle’s medium (Corning) supplemented with 10% EquaFETAL®, GlutaMAX® (2 mM), and penicillin–streptomycin (penicillin: 100 units mL−1; streptomycin: 100 µg mL−1). All cells were cultured at 37 °C under 5% CO2 and passaged before becoming fully confluent up to 20 passages. All cell lines were periodically tested for mycoplasma contamination. Cells were validated for the HER2 expression level in cell-based ELISA prior to use (see the “Cell-based ELISA assay” section).
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2

Cancer Cell Line Cultivation and Authentication

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The following cancer cell lines were obtained from the American Type
Culture Collection (Manassas, VA, USA): SK-BR-3, SK-OV-3, MDA-MB-453, and
MDA-MB-468. SK-BR-3 and SK-OV-3 cells were cultured in McCoy’s 5a medium,
whereas MDA-MB-453 and MDA-MB-468 cells were cultured in RPMI1640 medium. The
breast cancer cell line JIMT-1 was obtained from AddexBio and cultured in DMEM
medium. The HCC1954 cell line was a generous gift from Drs. Adi Gazdar, John
Minna, and Kenneth Huffman (Hamon Center for Therapeutic Oncology Research,
University of Texas Southwestern Medical Center at Dallas) and was cultured in
RPMI1640 medium. All media were supplemented with 1% penicillin/streptomycin, 1%
GlutaMAX (Thermo Fisher Scientific, Waltham, MA, USA), 1% sodium pyruvate and
10% fetal calf serum. The cell lines were tested monthly for mycoplasma
contamination and were authenticated annually at the University of Arizona
Genetics Core through DNA fingerprint analysis.
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3

Culturing Human Breast Cancer Cell Lines

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JIMT-1 (AddexBio), BT-474 (ATCC), and SKBR-3 (ATCC) were cultured in RPMI1640 (Corning) supplemented with 10% EquaFETAL® (Atlas Biologicals), GlutaMAX® (2 mM, Gibco), sodium pyruvate (1 mM, Corning), and penicillin-streptomycin (penicillin: 100 units mL–1; streptomycin: 100 µg mL–1, Gibco). KPL-4 (provided by Dr. Junichi Kurebayashi at Kawasaki Medical School)51 (link) and MDA-MB-231 (ATCC) were cultured in DMEM (Corning) supplemented with 10% EquaFETAL®, GlutaMAX®(2 mM), and penicillin-streptomycin (penicillin: 100 units mL–1; streptomycin: 100 µg mL–1). All cells were cultured at 37 °C under 5% CO2 and passaged before becoming fully confluent up to 10 passages. All cell lines were periodically tested for mycoplasma contamination. Cells were validated for the HER2 expression level in cell-based ELISA prior to use (see the following Cell-based ELISA section).
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4

Cell Culture Conditions for Cancer Research

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The T47D (cat# HTB-133), HEK293T (cat# CRL-3216), and MCF7 (cat# HTB-22) cells lines used for this study were purchased from ATCC and used at low passages. JIMT1 were purchased from AddexBio (cat# C0006005) and used at low passages. T47D and JIMT1 cells were maintained in RPMI 1640 with 10% FBS, 1% L-glutamine, and 1% penicillin-streptomycin. MCF7 cells were maintained in DF-12/DMEM Dulbecco medium with 10% FBS, 1% L-glutamine, and 1% penicillin-streptomycin. HEK293T cells were maintained in DMEM Dulbecco medium supplemented with 10% FBS, 1% L-glutamine and 1% penicillin-streptomycin. All cell lines were maintained under normal oxygen conditions (5% CO2, 37°C). When mentioned, MCF7 or T47D cells were hormonally deprived for 3 days in phenol-red-free DF12/DMEM or RPM1 media respectively that was supplemented with 5% charcoal/dextran-treated FCS. Following hormonal deprivation, the cells were treated with DMSO, E2 (100nm), BYL719 (1 μM), or both for 24 hours.
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5

Cell Culture Protocol for Breast Cancer Cell Lines

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BT-474, BT-474 clone 5 [99 (link)], and SK-BR-3 cells (American Type Culture Collection, Manassas, VA, USA) and JIMT-1 (AddexBio, San Diego, CA, USA) were cultured at 37 °C and 5% CO2 in phenol-red-free DMEM (Thermo Fischer Scientific, Cat# 3105303) supplemented with 10% fetal bovine serum (VWR, Cat# 97068-091, Radnor, PA, USA), 1 mM sodium pyruvate (Invitrogen, Cat# 11360070, Waltham, MA, USA), and 4 mM GlutaMAX (Thermo Fischer Scientific, Cat# 35050061). For imaging experiments, approximately 250,000 cells were seeded on coverslips previously coated with human fibronectin protein (50 µg/mL final concentration, R&D systems, Cat# 1918-FN-02M, Minneapolis, MN, USA).
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6

Cancer Cell Line Cultivation and Authentication

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The following cancer cell lines were obtained from the American Type
Culture Collection (Manassas, VA, USA): SK-BR-3, SK-OV-3, MDA-MB-453, and
MDA-MB-468. SK-BR-3 and SK-OV-3 cells were cultured in McCoy’s 5a medium,
whereas MDA-MB-453 and MDA-MB-468 cells were cultured in RPMI1640 medium. The
breast cancer cell line JIMT-1 was obtained from AddexBio and cultured in DMEM
medium. The HCC1954 cell line was a generous gift from Drs. Adi Gazdar, John
Minna, and Kenneth Huffman (Hamon Center for Therapeutic Oncology Research,
University of Texas Southwestern Medical Center at Dallas) and was cultured in
RPMI1640 medium. All media were supplemented with 1% penicillin/streptomycin, 1%
GlutaMAX (Thermo Fisher Scientific, Waltham, MA, USA), 1% sodium pyruvate and
10% fetal calf serum. The cell lines were tested monthly for mycoplasma
contamination and were authenticated annually at the University of Arizona
Genetics Core through DNA fingerprint analysis.
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7

Cell Line Acquisition and Authentication

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Cell lines BT-474, SK-BR-3, AU565, and MCF10A were purchased from and authenticated by American Type Culture Collection (Manassas, VA, USA), and were cultured based on the manufacturer’s recommendations. JIMT-1 was purchased and authenticated by Addexbio (San Diego, CA, USA). JIMT-1-Br3 was generously provided by Dr. Paul Lockman (West Virginia University School of Pharmacy, WV, USA) [26 (link)]. MCF10A-HER2-WT and MCF10A-Empty control were generously provided by Dr. Yehenew Agazie (Department of Biochemistry, West Virginia University School of Medicine, WV, USA) and were grown in medium, as previously described [27 (link)]. The cell lines were authenticated every 10–20 passages, and only low passage cells (2–6) were used for experiments. Cell medium supplements, including horse serum, EGF, penicillin and streptomycin, antibiotic/antimycotic, TrypLE, and trypsin, were purchased from Thermo Fisher Scientific, Waltham, MA, USA. FBS (fetal bovine serum) was purchased from VWR (Radnor, PA, USA). Insulin, cholera toxin, and hydrocortisone was purchased from Sigma-Aldrich (Sigma-Aldrich, St. Louis, MO, USA).
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8

Breast Cancer Cell Line Culture

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Breast cancer cell line, MDA-MB-231 was obtained from the American Type Culture Collection (ATCC, HTB-26, Manassas, VA, USA) and JIMT-1 was purchased by AddexBio (C0006005, San Diego, CA, USA). Cell lines were grown in a DMEM culture medium supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics/antimycotics (Gibco, 15240096, Waltham, MA, USA, penicillin 10,000 units/mL, streptomycin 10,000 μg/mL, amphotericin B 25 μg/mL). The cells were kept in humidified 95% air and 5% CO2 at 37 °C.
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9

Mammary Gland Fibroblast and Breast Cancer Cell Cultures

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All cells were maintained at 37 °C and 5 % CO2. Hunk+/+(Hunk WT)and Hunk/(Hunk KO) mammary gland fibroblasts (MGF) were isolated as previously described [5 (link)] and were grown in DMEM (Hyclone) supplemented with 10 % super calf serum (SCS, Gemini). BT474 (ATCC) human breast cancer cells were grown in RPMI-1640 (Hyclone) supplemented with 10 % fetal bovine serum (FBS, Gibco). BT474 cells expressing control or HUNK shRNA (gift from Lewis Chodosh, University of Pennsylvania) were generated and maintained as previously described [4 (link)]. JIMT-1 (Addex Bio) trastuzumab-resistant breast cancer cells were grown in DMEM (Hyclone) supplemented with 10 % FBS. JIMT-1 cells expressing control or HUNK shRNA were generated using the pGIPZ system (Thermo-GE/Dharmacon) and maintained in media containing 1 ug/ml puromycin. All media contained 2 mM glutamine (Thermo Scientific) and Penicillin/Streptomycin (Pen/Strep, Thermo Scientific) unless otherwise specified. pEGFP-LC3 was acquired through Addgene (plasmid #24920, provided by TorenFinkel [7 (link)] ). Transfection of GFP-LC3 was performed using Turbofect (Thermo Scientific).
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10

Investigating Breast Cancer Cell Lines

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All cells were maintained at 37°C and 5% CO2. BT474 cells were grown in RPMI-1640 (Corning) supplemented with 10% fetal bovine serum (FBS, Gibco). JIMT-1 (Addex Bio) cells were grown in DMEM (Corning) supplemented with 10% FBS. JIMT-1 cells expressing control or HUNK shRNA were generated as previously described [16 (link)]. All media contained 2 mM glutamine (Corning) and Penicillin/Streptomycin (Pen/Strep, Corning) unless otherwise specified. Inhibitors for AKT (AKt Inhibitor VIII), PLCγ (Et-18-OCH3), JNK (SP600125), PI3K (LY294002), SRC (PP2), mTORC1 (Rapamycin), p38 (SB 203580), JAK (AG 490), and c-RAF (ZM 336372) were purchased from EMD Millipore. Lapatinib was purchased from Santa Cruz.
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