Table 1.

Examples of screens performed to identify unknown factors of drug response, to suggest potential therapeutic strategies or to exploit novel screening concepts.

Selection	Screening method	Model	Identified genes – proof of concept	Identified genes – novel findings	Proposed mechanism	Remarks	Reference
Trastuzumab (HER2-targeting antibody)	shRNA screen (7,914 genes), positive selection	HER2-amplified breast cancer cell line BT474		PTEN	Loss of PTEN activates PI3K/AKT signaling	PI3K pathway activation as predictive marker	Berns et al. (2007)
Vemurafenib (PLX4032, BRAF inhibitor)	Kinome shRNA screen (535 genes), positive selection	Colorectal cancer cell line WiDr		EGFR	BRAF(V600E) inhibition activates EGFR and stimulates proliferation (feedback activation)	Melanoma cells express low levels of EGFR and are thus sensitive to BRAF inhibition; BRAF-mutant colon cancer might benefit from combination of BRAF and EGFR inhibitors	Prahallad et al. (2012)
Trastuzumab (HER2-targeting antibody)	shRNA screen (7,914 genes), positive selection	HER2-amplified breast cancer cell lines BT474, SKBR3 and HCC1954	PTEN	ARID1A	ARID1A loss activates ANXA1 which in turn activates AKT and causes resistance	High ANXA1 expression suggested as predictive marker	Berns et al. (2016)
Vemurafenib (BRAF inhibitor)	Genome-wide CRISPR/Cas9 screen (18,080 genes), positive selection	BRAF(V600E)-mutated melanoma cell line A375	NF1, MED12	NF2, CUL3, TADA1, TADA2B	TADA1 and TADA2 B (member of STAGA complex) recruit MED12 to c-myc to activate proliferation; MED12 activates TGF-βR signaling and MEK/ERK		Shalem et al. (2014)
Cytosine arabinoside (antimetabolite)	Genome-wide CRISPR/Cas9 screen (18,080 genes), positive selection	Acute myeloid leukemia cell line U937	DCK	SLC29A	Associated with nucleotide salvage pathway and required for the uptake and activation of Ara-C		Kurata et al. (2016)
6-thioguanine (antimetabolite)	Genome-wide CRISPR/Cas9 screen (19,150 genes), positive selection	Male mouse ES (JM8) cells	Mismatch repair genes (Mlh1, Msh2, Msh6, Pms2)	Hprt, GM15293, Letmd1, Olfr815, Prkg1, Tmem8c		Unknown candidate genes did not validate in subsequent in vitro experiments	Koike-Yusa et al. (2014)
6-thioguanine (antimetabolite)	Genome-wide CRISPR/Cas9 screen (7114 genes), positive selection	Human near-haploid chronic myeloid leukemia cell line KBM7	Mismatch repair genes (MSH2, MSH6, MLH1, PMS2)				Wang et al. (2014b)
Etoposide (DNA topoisomerase II inhibitor)	Genome-wide CRISPR/Cas9 screen (7114 genes), positive selection	Human pseudo-diploid leukemic HL60 and near-haploid KBM7 cell lines	TOP2A	CDK6	G1-cyclin dependent kinase involved in etoposide cytotoxicity		Wang et al. (2014b)
ATR inhibitor	Genome-wide CRISPR/Cas9 screen (19,150 genes), positive selection	Mouse ES cells (KH2)		CDC25A	CDC25A prevents cells from premature entry into mitosis	CDC25A levels could serve as criterion for patients more likely to respond; rationale to combine ATR and WEE1 inhibitor treatment	Ruiz et al. (2016)
Phenotypic selection	Genome-wide (18,543 human and 18,986 mouse genes) and focused (132 Ras-associated genes) CRISPR/Cas9 screen, negative selection	12 acute myeloid leukemia cell lines and NRAS-engineered mouse CGN Ba/F3 cell line		Several genes involved in Ras maturation or downstream of MAPK signaling pathway	Cancers driven by oncogenic Ras require Rac/PAK signaling to activate MAPK signaling	PAK inhibition as potential synthetic lethal therapeutic strategy in Ras-driven cancers	Wang et al. (2017)
Phenotypic selection	Genome-wide CRISPR/Cas9 screen (18,080 genes), negative selection	Glioblastoma stem-like and neural stem/progenitor cell lines		PKMYT1	PKMYT1, essential to inhibit cyclin B-CDK1 activity, is lost in glioblastoma	PKMYT1 inhibition as potential synthetic lethal therapeutic strategy in glioblastoma	Toledo et al. (2015)
Phenotypic selection	Genome-wide CRISPR/Cas9 screen (17,232 genes), negative selection	RNF43-mutant pancreatic ductal adenocarcinoma cell line	Components of Wnt pathway	FZD5	FZD5 encodes the main receptor for Wnt-β-catenin signaling in this context	FDZ5 inhibiton as a potential synthetic lethal therapeutic strategy in RNF43-mutated pancreatic cancer	Steinhart et al. (2017)
Phenotypic selection	Genome-wide (18,360 genes) and mini-pool (300 genes) CRISPR/Cas9 screen, quantitiative protein measurement of SQSTM1 modulators	Human neuroglioma H4 cell line	MTOR complex 1 and canonical macroautophagy components	Ufmylation components	Ufmylation induces SQSTM1 expression		Dejesus et al. (2016)
Lipopolysaccharide	Genome-wide CRISPR/Cas9 screen (21,786 genes), quantitative measurement of Tnf expression	Mouse bone-marrow derived dendritic cells	Tlr4, Myd88 (signal high), Zfp36 (signal low)	Components of OST complex, ER translocation pathway, PAF complex			Parnas et al. (2015)
Doxorubicin (DNA topoisomerase II inhibitor)	Viral gene-trap haploid screen, positive selection	Human haploid cell line HAP1	ABCB1, Keap1	SWI/SNF subunits, C9orf82, Eif4a1	SWI/SNF regulates Topoisomerase II activity, C9orf82 negatively regulates DNA repair	Patients with low SWI/SNF expression should not be treated with doxorubicin but rather aclarubicin or topotecan	Wijdeven et al. (2015)
Carboplatin (platinum drug)	Viral gene-trap haploid screen, positive selection	Human near-haploid chronic myeloid leukemia cell line KBM7		Components of volume-regulated anion channel (LRRC8D/LRRC8A)	50% of cellular platinum drug uptake mediated via LRRC8A/D channels	Downregulation of LRRC8 subunits could have an impact on platinum resistance	Planells-Cases et al. (2015)
6-thioguanine (antimetabolite)	piggyBac transposon haploid screen, positive selection	Mouse haploid ES cells	Mismatch repair genes (Msh2, Msh6, Mlh1)			Validation of loss-of-function screen	Pettitt et al. (2013)
Olaparib (PARP inhibitor)	piggyBac transposon haploid screen, positive selection	Mouse haploid ES cells		Parp1	Parp1 is a drug target and required for drug toxicity	Inhibited PAPR1 enzyme forms a toxic DNA lesion	Pettitt et al. (2013)
6-thioguanine (antimetabolite)	Viral gene-trap haploid screen, positive selection	Human near-haploid chronic myeloid leukemia cell line KBM7		HPRT	Enzyme converting 6-thioguanine to a toxic metabolite		Carette et al. (2009)
Imatinib (tyrosine-kinase inhibitor)	Viral gene-trap haploid screen, positive selection	Human near-haploid chronic myeloid leukemia cell line KBM7	NF1, PTPN1	PTPN12	Tyrosine phosphatase negatively regulates c-abl		Carette et al. (2009)
Formaldehyde	Viral gene-trap haploid screen, positive selection	Human near-haploid chronic myeloid leukemia cell line KBM7		12 candidate genes		6 out of 12 candidates validated	Shen et al. (2016)
Imatinib (tyrosine-kinase inhibitor)	Viral gene-trap haploid screen, positive selection	Human near-haploid chronic myeloid leukemia cell line KBM7		CASP10, CUX1, NF1, LYRM9, ZPBP, CEBPG		Only LYRM9 validated; only NF1 was also identified by Carette et al. (2009)	Shen et al. (2016)
MK-1775 (Wee1 inhibitor)	Viral gene-trap haploid screen, positive selection	Human near-haploid chronic myeloid leukemia cell line KBM7		SKP2,CUL1, CDK2 (among others)	Inactivation of S-phase can overcome Wee1 inhibitor resistance	Activity of DNA replication machinery could serve as selection criterion for Wee1 inhibitor treatment	Heijink et al. (2015)
Talazoparib (PARP inhibitor)	piggyBac transposon haploid screen, negative selection	Brca2-mutated mouse haploid ES cells (H129.2)		Ewsr1			Pettitt et al. (2017)
Phenotypic selection	Viral gene-trap haploid screen, quantitative protein measurement of AKT signaling	Human haploid cell line HAP1		KCTD5; GNB1 and other genes encoding Gβγ subunits	KCTD5 negatively regulates GPCR signaling by triggering proteolysis of dissociated Gβγ subunits		Brockmann et al. (2017)
Phenotypic selection	Viral gene-trap haploid screen, quantitative protein measurement of WNT signaling	Human haploid cell line HAP1 with 7TG-WNT reporter	Several known regulators	Genes linked to WNT receptor complex, CTNNB1 destruction complex and others	Other processes than CTNNB1 protein levels, e.g. truncation of domains, might regulate WNT signaling		Lebensohn et al. (2016)
Interferon-γ	Viral gene-trap haploid screen, quantitative protein measurement of PD-L1 abundance	Human haploid cell line HAP1	IFNγR-pathway, IRF1, CD274	CMTM6	CMTM6/4 enhances PD-L1-mediated T-cell inhibition, stabilizes PD-L1 protein level	Novel potential target for immune-suppressive cancer therapy	Mezzadra et al. (2017)
Phenotypic selection	Comparison of genome-wide CRISPR/Cas9 (19,050 genes) and viral gene-trap haploid screen, quantitative protein measurement of ER-associated degradation of MHC class I molecules	Human near-haploid chronic myeloid leukemia cell line KBM7 with MHC-I-ERAD reporter		TXNDC11	TXNDC11 encodes an EDEM2/3-associated disulphide reductase		Timms et al. (2016)
Phenotypic selection	Genome-wide CRISPR/Cas9 screen (20,611 genes), positive selection	Mouse non-small-cell lung cancer cell line transplanted into immunocompromised mice		Several candidate genes enriched in late primary tumors, high overlap of candidate genes in metastases	Enrichment of mutations in anti-apoptotic or other tumor suppressive pathways		Chen et al. (2015)
Monoclonal PD-1 antibody	Focused CRISPR/Cas9 screen (2,368 genes), positive selection	Mouse B16 melanoma cell line	CD47	Ptpn2, and several genes involved in four distinct biological processes	Loss of Ptpn2 sensitize tumors to immunotherapy through increased antigen presentation and T-cell stimulation	Inhibition of Ptpn2 as a therapeutic strategy to increase the effect of anti-PD-1 immunotherapy	Manguso et al. (2017)
Phenotypic selection	Mini CRISPR/Cas9 screen (10 genes), positive selection	3D mucociliary epithelial organoids from primary human basal cells		GRHL2	GRHL2 plays a key role in apical-basal cell polarity and epithelial morphogenesis		Gao et al. (2015)