Identification of Predictive <i>ERBB</i> Mutations by Leveraging Publicly Available Cell Line Databases

Koivu, Marika K.A.; Chakroborty, Deepankar; Tamirat, Mahlet Z.; Johnson, Mark S.; Kurppa, Kari J.; Elenius, Klaus

doi:10.1158/1535-7163.mct-20-0590

Cited by 6 publications

(12 citation statements)

References 52 publications

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“…In our recent work, we characterized a novel activating ERBB mutation located in the kinase dimerization interface, the ERBB2 E936K (56). ERBB2…”

Section: Discussionmentioning

confidence: 99%

“…To address the optimal conditions for a functional screen, the two expression libraries were transduced into murine lymphoid Ba/F3 cells that are dependent on exogenous IL3 for survival (54) but can be rendered IL3-independent by ectopic expression of oncogenic variants of a number of tyrosine kinases, including the ERBB receptors (55,56). After transduction, the Ba/F3 cells were cultured in puromycin for 48 hours to select for cells with stable expression.…”

Section: Setting Up a Functional Genetics Screen For Activating Erbb4 Variants In Ba/f3 Cellsmentioning

confidence: 99%

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An Unbiased Functional Genetics Screen Identifies Rare Activating ERBB4 Mutations

Chakroborty

Ojala

Knittle

et al. 2022

Cancer Research Communications

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Despite the relatively high frequency of somatic ERBB4 mutations in various cancer types, only a few activating ERBB4 mutations have been characterized, primarily due to lack of mutational hotspots in the ERBB4 gene. Here, we utilized our previously published pipeline, an in vitro screen for activating mutations, to perform an unbiased functional screen to identify potential activating ERBB4 mutations from a randomly mutated ERBB4 expression library. Ten potentially activating ERBB4 mutations were identified and subjected to validation by functional and structural analyses. Two of the 10 ERBB4 mutants, E715K and R687K, demonstrated hyperactivity in all tested cell models and promoted cellular growth under two-dimensional and three-dimensional culture conditions. ERBB4 E715K also promoted tumor growth in in vivo Ba/F3 cell mouse allografts. Importantly, all tested ERBB4 mutants were sensitive to the pan-ERBB tyrosine kinase inhibitors afatinib, neratinib, and dacomitinib. Our data indicate that rare ERBB4 mutations are potential candidates for ERBB4-targeted therapy with pan-ERBB inhibitors. Statement of Significance: ERBB4 is a member of the ERBB family of oncogenes that is frequently mutated in different cancer types but the functional impact of its somatic mutations remains unknown. Here, we have analyzed the function of over 8,000 randomly mutated ERBB4 variants in an unbiased functional genetics screen. The data indicate the presence of rare activating ERBB4 mutations in cancer, with potential to be targeted with clinically approved pan-ERBB inhibitors.

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“…In our recent work, we characterized a novel activating ERBB mutation located in the kinase dimerization interface, the ERBB2 E936K (56). ERBB2…”

Section: Discussionmentioning

confidence: 99%

Section: Setting Up a Functional Genetics Screen For Activating Erbb4 Variants In Ba/f3 Cellsmentioning

confidence: 99%

An Unbiased Functional Genetics Screen Identifies Rare Activating ERBB4 Mutations

Chakroborty

Ojala

Knittle

et al. 2022

Cancer Research Communications

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“…Cell culture Ba/F3 (DSMZ), NIH 3T3 (ATCC), and Phoenix Ampho cells (a gift from Dr. Garry Nolan) were cultured as previously described [27]. MCF-10A (ATCC) cells were cultured in DMEM/F-12 (Lonza) supplemented with 10% FCS, 50 U/ml penicillin, and 50 U/ml streptomycin, 20 ng/ml EGF (Peprotech), 0.5 mg/ml hydrocortisone (Sigma, #H-0888), 100 ng/ml cholera toxin (Sigma, #C-8052), and 10 µg/ml insulin (Sigma, #I-1882).…”

Section: Methodsmentioning

confidence: 99%

“…Phoenix Ampho cells were transfected with pBABE-based retroviral expression vectors encoding the ERBB proteins [27]. Retroviral infection with supernatants from Phoenix Ampho cells and selection to produce cell lines with stable ERBB3 expression was carried out, as previously described [25,27].…”

Section: Generation Of Cell Lines With Stable Erbb Expressionmentioning

confidence: 99%

Trans-activating mutations of the pseudokinase ERBB3

Elenius

Koivu

Chakroborty³

et al. 2023

Preprint

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Genetic changes in the ERBB family of receptor tyrosine kinases serve as oncogenic driver events and predictive biomarkers for ERBB inhibitor drugs. ERBB3 is a pseudokinase member of the family that, although lacking a fully active kinase domain, is well known for its potent signaling activity as a heterodimeric complex with ERBB2. Previous studies have identified few transforming ERBB3 mutations while the great majority of the hundreds of different somatic ERBB3 variants observed in different cancer types remain of unknown significance. Here, we describe an unbiased functional genetics screen of the transforming potential of thousands of ERBB3 mutations in parallel. The screen based on a previously described iSCREAM (in vitro screen of activating mutations) platform, and addressing ERBB3 pseudokinase signaling in a context of ERBB3/ERBB2 heterodimers, identified 18 hit mutations. Validation experiments in Ba/F3, NIH 3T3, and MCF10A cell backgrounds demonstrated the presence of both previously known and unknown transforming ERBB3 missense mutations functioning either as single variants or in cis as a pairwise combination. Drug sensitivity assays with trastuzumab, pertuzumab and neratinib indicated actionability of the transforming ERBB3 variants.

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“…Additionally, in the LUX-Lung 8 clinical trial, which included patients with stage IIIB/IV lung squamous cell carcinoma progressing after platinum-based chemotherapy, patients with ERBB4 mutations showed a trend toward better PFS [HR = 0.21 (0.02–1.94)] and OS [HR = 0.22 (0.05–1.04)] when treated with afatinib than erlotinib; however, the number of patients in this subgroup was small ( n = 14), and other treatment comparators were lacking 160 . Therefore, studies on the prevalence of HER4 genomic aberrations, their effects on tumor biology and treatment response to targeted agents (e.g., ~21% of TKI-sensitive ERBB -mutant cancer cell lines of different tumor entities exhibit ERBB4 deletions 177 ) and conventional chemotherapy, as well as on optimal treatment modalities, should be systematically performed in patients with NSCLC in the future, e.g., in the form of a world-wide registry trial similar to the eNRG trials. Table 4 summarizes clinical outcomes and trials in patients with NSCLC bearing HER3, HER4 and NRG alterations.…”

Section: The Her4 (Erbb4) Receptormentioning

confidence: 99%

Targeting the EGF receptor family in non-small cell lung cancer—increased complexity and future perspectives

et al. 2022

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Lung cancer remains the leading cause of cancer-associated mortality worldwide, but with the emergence of oncogene targeted therapies, treatment options have tremendously improved. Owing to their biological relevance, members of the ERBB receptor family, including the EGF receptor (EGFR), HER2, HER3 and HER4, are among the best studied oncogenic drivers. Activating EGFR mutations are frequently observed in non-small cell lung cancer (NSCLC), and small molecule tyrosine kinase inhibitors (TKIs) are the established first line treatment option for patients whose tumors bear “typical/classical” EGFR mutations (exon 19 deletions, L858R point mutations). Additionally, new TKIs are rapidly evolving with better efficacy to overcome primary and secondary treatment resistance (e.g., that due to T790M or C797S resistance mutations). Some atypical EGFR mutations, such as the most frequent exon 20 insertions, exhibit relative resistance to earlier generation TKIs through steric hindrance. In this subgroup, newer TKIs, such as mobocertinib and the bi-specific antibody amivantamab have recently been approved, whereas less frequent atypical EGFR mutations remain understudied. In contrast to EGFR, HER2 has long remained a challenging target, but better structural understanding has led to the development of newer generations of TKIs. The recent FDA approval of the antibody-drug conjugate trastuzumab-deruxtecan for pretreated patients with HER2 mutant NSCLC has been an important therapeutic breakthrough. HER3 and HER4 also exert oncogenic potential, and targeted treatment approaches are being developed, particularly for HER3. Overall, strategies to inhibit the oncogenic function of ERBB receptors in NSCLC are currently evolving at an unprecedented pace; therefore, this review summarizes current treatment standards and discusses the outlook for future developments.

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Identification of Predictive ERBB Mutations by Leveraging Publicly Available Cell Line Databases

Cited by 6 publications

References 52 publications

An Unbiased Functional Genetics Screen Identifies Rare Activating ERBB4 Mutations

An Unbiased Functional Genetics Screen Identifies Rare Activating ERBB4 Mutations

Trans-activating mutations of the pseudokinase ERBB3

Targeting the EGF receptor family in non-small cell lung cancer—increased complexity and future perspectives

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