bims-pimaco 2021-04-11 papers

on PI3K and MAPK signalling in colorectal cancer

Issue of 2021–04–11
thirteen papers selected by
Lucas B. Zeiger, CRUK Scotland Institute, Beatson Institute for Cancer Research

Mutant KRAS triggers functional reprogramming of tumor-associated macrophages in colorectal cancer.
TSC-insensitive Rheb mutations induce oncogenic transformation through a combination of constitutively active mTORC1 signalling and proteome remodelling.
Signaling Pathways Involved in Nutrient Sensing Control in Cancer Stem Cells: An Overview.
Role of thyroid hormone-integrin αvβ3-signal and therapeutic strategies in colorectal cancers.
Ras sumoylation in cell signaling and transformation.
A liquid culture cancer spheroid model reveals low PI3K/Akt pathway activity and low adhesiveness to the extracellular matrix.
EGFR Amplification in Metastatic Colorectal Cancer.
A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.
Mechanisms of Resistance to KRASG12C-Targeted Therapy.
N-3 Polyunsaturated fatty acid ethyl esters decrease the invasion, but not the proliferation, of human colorectal cancer cells via a PI3K-dependent mechanism in vitro.
Clinical acquired resistance to KRASG12C inhibition through a novel KRAS switch-II pocket mutation and polyclonal alterations converging on RAS-MAPK reactivation.
An updated patent review of Akt inhibitors (2016-present).
Identification of PIK3CA multigene mutation patterns associated with superior prognosis in stomach cancer.

Signal Transduct Target Ther. 2021 Apr 09. 6(1): 144

Mutant KRAS triggers functional reprogramming of tumor-associated macrophages in colorectal cancer.

Huashan Liu, Zhenxing Liang, Chi Zhou, Ziwei Zeng, Fengwei Wang, Tuo Hu, Xiaowen He, Xiaojian Wu, Xianrui Wu, Ping Lan.

Oncogenic KRAS has been previously identified to act in a cell-intrinsic manner to modulate multiple biological functions of colorectal cancer (CRC). Here, we demonstrate a cell-extrinsic role of KRAS, where KRAS engages with the tumor microenvironment by functional reprogramming of tumor-associated macrophages (TAMs). In human CRC specimens, mutant KRAS positively correlates with the presence of TAMs. Mutationally activated KRAS in tumor cells reprograms macrophages to a TAM-like phenotype via a combination effect of tumor-derived CSF2 and lactate. In turn, KRAS-reprogrammed macrophages were shown to not only promote tumor progression but also induce the resistance of tumor cells to cetuximab therapy. Mechanistically, KRAS drives the production of CSF2 and lactate in tumor cells by stabilizing hypoxia-inducible factor-1α (HIF-1α), a transcription factor that controls the expression of CSF2 and glycolytic genes. Mutant KRAS increased the production of reactive oxygen species, an inhibitor of prolyl hydroxylase activity which decreases HIF-1α hydroxylation, leading to enhanced HIF-1α stabilization. This cell-extrinsic mechanism awards KRAS a critical role in engineering a permissive microenvironment to promote tumor malignancy, and may present new insights on potential therapeutic defense strategies against mutant KRAS tumors.

DOI: https://doi.org/10.1038/s41392-021-00534-2
Cell Mol Life Sci. 2021 Apr 08.

TSC-insensitive Rheb mutations induce oncogenic transformation through a combination of constitutively active mTORC1 signalling and proteome remodelling.

Jianling Xie, Stuart P De Poi, Sean J Humphrey, Leanne K Hein, John B Bruning, Wenru Pan, Luke A Selth, Timothy J Sargeant, Christopher G Proud.

  The mechanistic target of rapamycin complex 1 (mTORC1) is an important regulator of cellular metabolism that is commonly hyperactivated in cancer. Recent cancer genome screens have identified multiple mutations in Ras-homolog enriched in brain (Rheb), the primary activator of mTORC1 that might act as driver oncogenes by causing hyperactivation of mTORC1. Here, we show that a number of recurrently occurring Rheb mutants drive hyperactive mTORC1 signalling through differing levels of insensitivity to the primary inactivator of Rheb, tuberous sclerosis complex. We show that two activated mutants, Rheb-T23M and E40K, strongly drive increased cell growth, proliferation and anchorage-independent growth resulting in enhanced tumour growth in vivo. Proteomic analysis of cells expressing the mutations revealed, surprisingly, that these two mutants promote distinct oncogenic pathways with Rheb-T23M driving an increased rate of anaerobic glycolysis, while Rheb-E40K regulates the translation factor eEF2 and autophagy, likely through differential interactions with 5' AMP-activated protein kinase (AMPK) which modulate its activity. Our findings suggest that unique, personalized, combination therapies may be utilised to treat cancers according to which Rheb mutant they harbour.

Keywords:  AMPK; PKM; Rheb; TSC; eEF2; mTOR

DOI:  https://doi.org/10.1007/s00018-021-03825-7
Front Endocrinol (Lausanne). 2021 ;12 627745

Signaling Pathways Involved in Nutrient Sensing Control in Cancer Stem Cells: An Overview.

Martha Robles-Flores, Angela P Moreno-Londoño, M Cristina Castañeda-Patlán.

  Cancer cells characteristically have a high proliferation rate. Because tumor growth depends on energy-consuming anabolic processes, including biosynthesis of protein, lipid, and nucleotides, many tumor-associated conditions, including intermittent oxygen deficiency due to insufficient vascularization, oxidative stress, and nutrient deprivation, results from fast growth. To cope with these environmental stressors, cancer cells, including cancer stem cells, must adapt their metabolism to maintain cellular homeostasis. It is well- known that cancer stem cells (CSC) reprogram their metabolism to adapt to live in hypoxic niches. They usually change from oxidative phosphorylation to increased aerobic glycolysis even in the presence of oxygen. However, as opposed to most differentiated cancer cells relying on glycolysis, CSCs can be highly glycolytic or oxidative phosphorylation-dependent, displaying high metabolic plasticity. Although the influence of the metabolic and nutrient-sensing pathways on the maintenance of stemness has been recognized, the molecular mechanisms that link these pathways to stemness are not well known. Here in this review, we describe the most relevant signaling pathways involved in nutrient sensing and cancer cell survival. Among them, Adenosine monophosphate (AMP)-activated protein kinase (AMPK) pathway, mTOR pathway, and Hexosamine Biosynthetic Pathway (HBP) are critical sensors of cellular energy and nutrient status in cancer cells and interact in complex and dynamic ways.

Keywords:  adenosine monophosphate-activated protein kinase (AMPK) signaling; cancer stem cells; hexosamine biosynthesis pathway (HBP) pathway; mammalian target of rapamycin (mTOR) signaling; nutrient sensing

DOI:  https://doi.org/10.3389/fendo.2021.627745
J Biomed Sci. 2021 Apr 08. 28(1): 24

Role of thyroid hormone-integrin αvβ3-signal and therapeutic strategies in colorectal cancers.

Yu-Chen S H Yang, Po-Jui Ko, Yi-Shin Pan, Hung-Yun Lin, Jacqueline Whang-Peng, Paul J Davis, Kuan Wang.

  Thyroid hormone analogues-particularly, L-thyroxine (T4) has been shown to be relevant to the functions of a variety of cancers. Integrin αvβ3 is a plasma membrane structural protein linked to signal transduction pathways that are critical to cancer cell proliferation and metastasis. Thyroid hormones, T4 and to a less extend T3 bind cell surface integrin αvβ3, to stimulate the extracellular signal-regulated kinase 1/2 (ERK1/2) pathway to stimulate cancer cell growth. Thyroid hormone analogues also engage in crosstalk with the epidermal growth factor receptor (EGFR)-Ras pathway. EGFR signal generation and, downstream, transduction of Ras/Raf pathway signals contribute importantly to tumor cell progression. Mutated Ras oncogenes contribute to chemoresistance in colorectal carcinoma (CRC); chemoresistance may depend in part on the activity of ERK1/2 pathway. In this review, we evaluate the contribution of thyroxine interacting with integrin αvβ3 and crosstalking with EGFR/Ras signaling pathway non-genomically in CRC proliferation. Tetraiodothyroacetic acid (tetrac), the deaminated analogue of T4, and its nano-derivative, NDAT, have anticancer functions, with effectiveness against CRC and other tumors. In Ras-mutant CRC cells, tetrac derivatives may overcome chemoresistance to other drugs via actions initiated at integrin αvβ3 and involving, downstream, the EGFR-Ras signaling pathways.

Keywords:  Colorectal Cancer; Epidermal growth factor receptor; Integrin αvβ3; NDAT; Ras mutation

DOI:  https://doi.org/10.1186/s12929-021-00719-5
Semin Cancer Biol. 2021 Apr 01. pii: S1044-579X(21)00083-3. [Epub ahead of print]

Ras sumoylation in cell signaling and transformation.

Wei Dai, Suqing Xie, Changyan Chen, Byeong Hyeok Choi.

  Ras proteins are small GTPases that participate in multiple signal cascades, regulating crucial cellular processes including cell survival, proliferation, and differentiation. Mutations or deregulated activities of Ras are frequently the driving force for oncogenic transformation and tumorigenesis. Posttranslational modifications play a crucial role in mediating the stability, activity, or subcellular localization/trafficking of numerous cellular regulators including Ras proteins. A series of recent studies reveal that Ras proteins are also regulated by sumoylation. All three Ras protein isoforms (HRas, KRas, and NRas) are modified by SUMO3. The conserved lysine42 appears to be the primary site for mediating sumoylation. Expression of KRasV12/R42 mutants compromised the activation of the Raf/MEK/ERK signaling axis, leading to a reduced rate of cell migration and invasion in vitro in multiple cell lines. Moreover, treatment of transformed pancreatic cells with a SUMO E2 inhibitor blocks cell migration in a concentration-dependent manner, which is associated with a reduced level of both KRas sumoylation and expression of mesenchymal cell markers. Furthermore, mouse xenograft experiments reveal that expression of a SUMO-resistant mutant appears to suppress tumor development in vivo. Combined, these studies indicate that sumoylation functions as an important mechanism in mediating the roles of Ras in cell proliferation, differentiation, and malignant transformation and that the SUMO-modification system of Ras oncoproteins can be explored as a new druggable target for various human malignancies.

Keywords:  Oncogene; Posttranslational modifications; Ras; Sumoylation; Transformation

DOI:  https://doi.org/10.1016/j.semcancer.2021.03.033
FEBS J. 2021 Apr 09.

A liquid culture cancer spheroid model reveals low PI3K/Akt pathway activity and low adhesiveness to the extracellular matrix.

Natsuki Abe-Fukasawa, Rina Watanabe, Yuki Gen, Taito Nishino, Nobue Itasaki.

  Three-dimensional (3D) cultures of cancer cells in liquid without extracellular matrix (ECM) offers in vitro models for metastasising conditions such as those in vessels and effusion. However, liquid culturing is often hindered by cell adhesiveness, which causes large cell clumps. We previously described a liquid culture material, LA717, which prevents non-clonal cell adhesion and subsequent clumping, thus allowing clonal growth of spheroids in an anchorage-independent manner. Here, we examined such liquid culture cancer spheroids for the acquisition of apical-basal polarity, sensitivity to an Akt inhibitor (anticancer drug MK-2206) and interaction with ECM. The spheroids present apical plasma membrane on the surface, which originated from the failure of polarisation at the single-cell stage and subsequent defects in phosphorylated Ezrin accumulation at the cell boundary during the first cleavage, failing internal lumen formation. At the multi-cellular stage, liquid culture spheroids presented bleb-like protrusion on the surface, which was enhanced by activation of the PI3K/Akt pathway and reduced by PI3K/Akt inhibitors. Liquid culture spheroids exhibited slow proliferation speed and low endogenous pAkt levels compared to gel-cultured spheroids and 2D-cultured cells, explaining the susceptibility to the Akt-inhibiting anticancer drug. Subcutaneous xenografting and in vitro analysis demonstrated low viability and adhesive property of liquid culture spheroids to ECM, while migratory and invasive capacities were comparable with gel-cultured spheroids. These features agree with the low efficacy of circulating tumour spheroids in the settling step of metastasis. This study demonstrates the feature of anchorage-independent spheroids and validates liquid cultures as a useful method in cancer spheroid research.

Keywords:  3D culture; anchorage-independent; apical-basal polarity; cancer; spheroid

DOI:  https://doi.org/10.1111/febs.15867
J Natl Cancer Inst. 2021 Apr 07. pii: djab069. [Epub ahead of print]

EGFR Amplification in Metastatic Colorectal Cancer.

Giovanni Randon, Rona Yaeger, Jaclyn F Hechtman, Paolo Manca, Giovanni Fucà, Henry Walch, Jeeyun Lee, Elena Élez, Jenny Seligmann, Benedetta Mussolin, Filippo Pagani, Marco Maria Germani, Margherita Ambrosini, Daniele Rossini, Margherita Ratti, Francesc Salvà, Susan D Richman, Henry Wood, Gouri Nanjangud, Annunziata Gloghini, Massimo Milione, Alberto Bardelli, Filippo de Braud, Federica Morano, Chiara Cremolini, Filippo Pietrantonio.

   BACKGROUND: EGFR amplification occurs in about 1% of metastatic colorectal cancers (mCRCs) but is not routinely tested as a prognostic or predictive biomarker for patients treated with anti-EGFR monoclonal antibodies (mAbs). Herein, we aimed to characterize the clinical and molecular landscape of EGFR-amplified metastatic colorectal cancer (mCRC).
METHODS: In this multinational cohort study, we compared clinical data of 62 patients with EGFR-amplified vs. 1459 EGFR non-amplified mCRC, as well as comprehensive genomic data of 35 EGFR-amplified vs. 439 EGFR non-amplified RAS/BRAF wild-type and microsatellite stable (MSS) tumor samples.
RESULTS: EGFR amplification was statistically significantly associated with left primary tumor sidedness and RAS/BRAF wild-type status. All EGFR-amplified tumors were MSS and HER2 non-amplified. Overall, EGFR-amplified samples had higher median fraction of genome altered compared to EGFR non-amplified, RAS/BRAF wild-type MSS cohort. Patients with EGFR-amplified tumors reported longer overall survival (OS) (median OS = 71.3 months; 95% confidence interval [CI] = 50.7-NA) vs. EGFR non-amplified ones (24.0 months; 95% CI = 22.8-25.6; hazard ratio [HR] = 0.30, 95% CI = 0.20-0.44, P<.001; adjusted HR = 0.46, 95%CI = 0.30-0.69, P<.001). In the subgroup of patients with RAS/BRAF wild-type mCRC exposed to anti-EGFR-based therapy, EGFR amplification was again associated with better OS (median OS = 54.0 months [95% CI = 35.2-NA] vs. 29.1 months [95% CI = 27.0-31.9], respectively; HR = 0.46, 95%CI = 0.28-0.76, P=.002).
CONCLUSION: Patients with EGFR-amplified mCRC represent a biologically defined subgroup and merit dedicated clinical trials with novel and more potent EGFR targeting strategies beyond single-agent monoclonal antibodies.

Keywords:   EGFR amplification; anti-EGFR monoclonal antibodies; metastatic colorectal cancer; molecular subgroups; prognosis

DOI:  https://doi.org/10.1093/jnci/djab069
Open Biol. 2021 Apr;11(4): 200405

A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.

Lenka Halova, David Cobley, Mirita Franz-Wachtel, Tingting Wang, Kaitlin R Morrison, Karsten Krug, Nicolas Nalpas, Boris Maček, Iain M Hagan, Sean J Humphrey, Janni Petersen.

  Fluctuations in TOR, AMPK and MAP-kinase signalling maintain cellular homeostasis and coordinate growth and division with environmental context. We have applied quantitative, SILAC mass spectrometry to map TOR and nutrient-controlled signalling in the fission yeast Schizosaccharomyces pombe. Phosphorylation levels at more than 1000 sites were altered following nitrogen stress or Torin1 inhibition of the TORC1 and TORC2 networks that comprise TOR signalling. One hundred and thirty of these sites were regulated by both perturbations, and the majority of these (119) new targets have not previously been linked to either nutritional or TOR control in either yeasts or humans. Elimination of AMPK inhibition of TORC1, by removal of AMPKα (ssp2::ura4+), identified phosphosites where nitrogen stress-induced changes were independent of TOR control. Using a yeast strain with an ATP analogue-sensitized Cdc2 kinase, we excluded sites that were changed as an indirect consequence of mitotic control modulation by nitrogen stress or TOR signalling. Nutritional control of gene expression was reflected in multiple targets in RNA metabolism, while significant modulation of actin cytoskeletal components points to adaptations in morphogenesis and cell integrity networks. Reduced phosphorylation of the MAPKK Byr1, at a site whose human equivalent controls docking between MEK and ERK, prevented sexual differentiation when resources were sparse but not eliminated.

Keywords:  Byr1 MAPKK; TORC1; TORC2; fission yeast Schizosaccharomyces pombe; nitrogen stress; phosphoproteome

DOI:  https://doi.org/10.1098/rsob.200405
Cancer Discov. 2021 Apr 05.

Mechanisms of Resistance to KRASG12C-Targeted Therapy.

Neal S Akhave, Amadeo B Biter, David S Hong.

KRAS mutations are among the most common drivers of human carcinogenesis, and are associated with poor prognosis and an aggressive disease course. With the advent of KRASG12C inhibitors, the RAS protein is now targetable, with such inhibitors showing marked clinical responses across multiple tumor types. However, these responses are short-lived due to the development of resistance. Preclinical studies now suggest MAPK reactivation, stimulation of CDK4/6-dependent cell-cycle transition, and immune defects as possible mechanisms of resistance. Devising strategies to overcome such resistance mechanisms, which are a barrier to long-term clinical response, remain an active area of research. SIGNIFICANCE: Although KRAS-targeted cancer therapy is revolutionary, tumors rapidly develop resistance. Understanding the mechanisms driving this resistance and designing combination strategies to overcome it are integral to achieving long-term disease control.

DOI: https://doi.org/10.1158/2159-8290.CD-20-1616
Prostaglandins Leukot Essent Fatty Acids. 2021 Mar 24. pii: S0952-3278(21)00036-3. [Epub ahead of print]167 102273

N-3 Polyunsaturated fatty acid ethyl esters decrease the invasion, but not the proliferation, of human colorectal cancer cells via a PI3K-dependent mechanism in vitro.

Eric Pfister, Rebecca Smith, Michelle A Lane.

  N-3 polyunsaturated fatty acid (PUFA) ethyl esters have been approved by the FDA for the treatment of dyslipidemia and are promising cancer therapeutics. The study objectives were to determine if and how n-3 PUFA ethyl esters affected the proliferation and invasion of colorectal cancer cells. SW620 and HCT-116 parental and HCT-116 mutant cells isogenic for constitutively active PI3K were treated with free or ethyl esterified n-3 PUFAs and counted 72 h later. Cells were also administered n-3 PUFA ethyl esters to determine if these compounds decreased invasion through Boyden chambers and PI3K activity via western blot analysis of phosphorylated Akt. Free and n-3 PUFA ethyl esters decreased the proliferation of all cell lines. The invasion and Akt phosphorylation of both parental cell lines was decreased following treatment but this did not occur in mutant cells. The ability of n-3 PUFA ethyl esters to decrease proliferation and invasion in vitro indicates these compounds may be effective in vivo.

Keywords:  Colorectal cancer; Metastasis; N-3 polyunsaturated fatty acids; Phosphatidylinositol 3-kinase

DOI:  https://doi.org/10.1016/j.plefa.2021.102273
Cancer Discov. 2021 Apr 06. pii: candisc.0365.2021. [Epub ahead of print]

Clinical acquired resistance to KRASG12C inhibition through a novel KRAS switch-II pocket mutation and polyclonal alterations converging on RAS-MAPK reactivation.

Noritaka Tanaka, Jessica J Lin, Chendi Li, Meagan B Ryan, Junbing Zhang, Lesli A Kiedrowski, Alexa G Michel, Mohammed U Syed, Katerina A Fella, Mustafa Sakhi, Islam Baiev, Dejan Juric, Justin F Gainor, Samuel J Klempner, Jochen K Lennerz, Giulia Siravegna, Liron Bar-Peled, Aaron N Hata, Rebecca S Heist, Ryan B Corcoran.

Mutant-selective KRASG12C inhibitors, such as MRTX849 (adagrasib) and AMG 510 (sotorasib), have demonstrated efficacy in KRASG12C-mutant cancers including non-small cell lung cancer (NSCLC). However, mechanisms underlying clinical acquired resistance to KRASG12C inhibitors remain undetermined. To begin to define the mechanistic spectrum of acquired resistance, we describe a KRASG12C NSCLC patient who developed polyclonal acquired resistance to MRTX849 with the emergence of 10 heterogeneous resistance alterations in serial cell-free DNA spanning four genes (KRAS, NRAS, BRAF, MAP2K1), all of which converge to reactivate RAS-MAPK signaling. Notably, a novel KRASY96D mutation affecting the switch-II pocket, to which MRTX849 and other inactive-state inhibitors bind, was identified that interferes with key protein-drug interactions and confers resistance to these inhibitors in engineered and patient-derived KRASG12C cancer models. Interestingly, a novel, functionally distinct tri-complex KRASG12C active-state inhibitor RM-018 retained the ability to bind and inhibit KRASG12C/Y96D and could overcome resistance.

DOI: https://doi.org/10.1158/2159-8290.CD-21-0365
Expert Opin Ther Pat. 2021 Apr 09.

An updated patent review of Akt inhibitors (2016-present).

Yu Guo, Yizhen Jin, Bingxue Qu, Yu Zhang, Jinxin Che, Xiaowu Dong.

   INTRODUCTION: : Akt is a widely-known serine threonine kinase involved in a series of critical cellular pathways like cell survival and proliferation. With the development of small-molecule Akt inhibitors, new strategies such as covalent, peptide-based, and PROTAC (Proteolysis Targeting Chimera) strategies have also been used the design of Akt inhibitors. On the other hand, due to the specificity of the Akt pathway, the use of Akt modulators in combination therapy and immunotherapy has been disclosed in the past 5 years.
AREAS COVERED: : This review focuses on the patent literature covering small molecule inhibitors of Akt kinase and their applications from 2016-present.
EXPERT OPINION: : Although Akt inhibitors' progress has been somewhat slow over the past five years, new strategies still provide new opportunities for the development of Akt inhibitors. Combination with Akt pathway inhibitors for tumor therapy has also been widely disclosed in patents in the last five years. Notably, combination strategies of Akt inhibitors and immunotherapy have started to emerge in recent years. While the clinical indications of Akt modulators should not be limited to anti-cancer, it is still worth trying the treatment of other diseases. Within the next years, current drug development around Akt inhibitors should be fascinating.

Keywords:  Akt; cancer; clinical trial; indications; inhibitors; new strategies; patents

DOI:  https://doi.org/10.1080/13543776.2021.1915291
BMC Cancer. 2021 Apr 07. 21(1): 368

Identification of PIK3CA multigene mutation patterns associated with superior prognosis in stomach cancer.

Yu Yu, Zhuoming Xie, Mingxin Zhao, Xiaohua Lian.

   BACKGROUND: PIK3CA is the second most frequently mutated gene in cancers and is extensively studied for its role in promoting cancer cell resistance to chemotherapy or targeted therapy. However, PIK3CA functions have mostly been investigated at a lower-order genetic level, and therapeutic strategies targeting PIK3CA mutations have limited effects. Here, we explore crucial factors interacting with PIK3CA mutations to facilitate a significant marginal survival effect at the higher-order level and identify therapeutic strategies based on these marginal factors.
METHODS: Mutations in stomach adenocarcinoma (STAD), breast adenocarcinoma (BRCA), and colon adenocarcinoma (COAD) samples from The Cancer Genome Atlas (TCGA) database were top-selected and combined for Cox proportional-hazards model analysis to calculate hazard ratios of mutation combinations according to overall survival data and define criteria to acquire mutation combinations with considerable marginal effects. We next analyzed the PIK3CA + HMCN1 + LRP1B mutation combination with marginal effects in STAD patients by Kaplan-Meier, transcriptomic differential, and KEGG integrated pathway enrichment analyses. Lastly, we adopted a connectivity map (CMap) to find potentially useful drugs specifically targeting LRP1B mutation in STAD patients.
RESULTS: Factors interacting with PIK3CA mutations in a higher-order manner significantly influenced patient cohort survival curves (hazard ratio (HR) = 2.93, p-value = 2.63 × 10- 6). Moreover, PIK3CA mutations interacting with higher-order combination elements distinctly differentiated survival curves, with or without a marginal factor (HR = 0.26, p-value = 6.18 × 10- 8). Approximately 3238 PIK3CA-specific higher-order mutational combinations producing marginal survival effects were obtained. In STAD patients, PIK3CA + HMCN1 mutation yielded a substantial beneficial survival effect by interacting with LRP1B (HR = 3.78 × 10- 8, p-value = 0.0361) and AHNAK2 (HR = 3.86 × 10- 8, p-value = 0.0493) mutations. We next identified 208 differentially expressed genes (DEGs) induced by PIK3CA + HMCN1 compared with LRP1B mutation and mapped them to specific KEGG modules. Finally, small-molecule drugs such as geldanamycin (connectivity score = - 0.4011) and vemurafenib (connectivity score = - 0.4488) were selected as optimal therapeutic agents for targeting the STAD subtype with LRP1B mutation.
CONCLUSIONS: Overall, PIK3CA-induced marginal survival effects need to be analyzed. We established a framework to systematically identify crucial factors responsible for marginal survival effects, analyzed mechanisms underlying marginal effects, and identified related drugs.

Keywords:  Cancer prognosis; Higher-order genetic interaction; Marginal effect; PIK3CA mutation; Stomach adenocarcinoma

DOI:  https://doi.org/10.1186/s12885-021-08115-w