scholarly journals Loss-of-function, gain-of-function and dominant-negative mutations have profoundly different effects on protein structure: implications for variant effect prediction

2021 ◽  
Author(s):  
Lukas Gerasimavicius ◽  
Benjamin J Livesey ◽  
Joseph A Marsh

Most known pathogenic mutations occur in protein-coding regions of DNA and change the way proteins are made. Taking protein structure into account has therefore provided great insight into the molecular mechanisms underlying human genetic disease. While there has been much focus on how mutations can disrupt protein structure and thus cause a loss of function (LOF), alternative mechanisms, specifically dominant-negative (DN) and gain-of-function (GOF) effects, are less understood. Here, we have investigated the protein-level effects of pathogenic missense mutations associated with different molecular mechanisms. We observe striking differences between recessive vs dominant, and LOF vs non-LOF mutations, with dominant, non-LOF disease mutations having much milder effects on protein structure, and DN mutations being highly enriched at protein interfaces. We also find that nearly all computational variant effect predictors underperform on non-LOF mutations, even those based solely on sequence conservation. However, we do find that non-LOF mutations could potentially be identified by their tendency to cluster in space. Overall, our work suggests that many pathogenic mutations that act via DN and GOF mutations are likely being missed by current variant prioritisation strategies, but that there is considerable scope to improve computational predictions through consideration of molecular disease mechanisms.

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Lukas Gerasimavicius ◽  
Xin Liu ◽  
Joseph A. Marsh

Abstract Attempts at using protein structures to identify disease-causing mutations have been dominated by the idea that most pathogenic mutations are disruptive at a structural level. Therefore, computational stability predictors, which assess whether a mutation is likely to be stabilising or destabilising to protein structure, have been commonly used when evaluating new candidate disease variants, despite not having been developed specifically for this purpose. We therefore tested 13 different stability predictors for their ability to discriminate between pathogenic and putatively benign missense variants. We find that one method, FoldX, significantly outperforms all other predictors in the identification of disease variants. Moreover, we demonstrate that employing predicted absolute energy change scores improves performance of nearly all predictors in distinguishing pathogenic from benign variants. Importantly, however, we observe that the utility of computational stability predictors is highly heterogeneous across different proteins, and that they are all inferior to the best performing variant effect predictors for identifying pathogenic mutations. We suggest that this is largely due to alternate molecular mechanisms other than protein destabilisation underlying many pathogenic mutations. Thus, better ways of incorporating protein structural information and molecular mechanisms into computational variant effect predictors will be required for improved disease variant prioritisation.


2020 ◽  
Author(s):  
Lukas Gerasimavicius ◽  
Xin Liu ◽  
Joseph A Marsh

AbstractAttempts at using protein structures to identify disease-causing mutations have been dominated by the idea that most pathogenic mutations are disruptive at a structural level. Therefore, computational stability predictors, which assess whether a mutation is likely to be stabilising or destabilising to protein structure, have been commonly used when evaluating new candidate disease variants, despite not having been developed specifically for this purpose. We therefore tested 12 different stability predictors for their ability to discriminate between pathogenic and putatively benign missense variants. We find that one method, FoldX, considerably outperforms all others in the identification of disease variants. Moreover, we demonstrate that employing absolute energy change scores improves performance of nearly all predictors. Importantly, however, we observe that the utility of computational stability predictors is highly heterogeneous across different proteins, and that they are all are inferior to the best performing variant effect predictors for identifying pathogenic mutations. We suggest that this is largely due to alternate molecular mechanisms other than protein destabilisation underlying many pathogenic mutations. Thus, better ways of incorporating protein structural information and molecular mechanisms into computational variant effect predictors will be required for improved disease variant prioritisation.


2015 ◽  
Vol 33 (21) ◽  
pp. 2345-2352 ◽  
Author(s):  
Gaëlle Bougeard ◽  
Mariette Renaux-Petel ◽  
Jean-Michel Flaman ◽  
Camille Charbonnier ◽  
Pierre Fermey ◽  
...  

Purpose The aim of the study was to update the description of Li-Fraumeni syndrome (LFS), a remarkable cancer predisposition characterized by extensive clinical heterogeneity. Patients and Methods From 1,730 French patients suggestive of LFS, we identified 415 mutation carriers in 214 families harboring 133 distinct TP53 alterations and updated their clinical presentation. Results The 322 affected carriers developed 552 tumors, and 43% had developed multiple malignancies. The mean age of first tumor onset was 24.9 years, 41% having developed a tumor by age 18. In childhood, the LFS tumor spectrum was characterized by osteosarcomas, adrenocortical carcinomas (ACC), CNS tumors, and soft tissue sarcomas (STS) observed in 30%, 27%, 26%, and 23% of the patients, respectively. In adults, the tumor distribution was characterized by the predominance of breast carcinomas observed in 79% of the females, and STS observed in 27% of the patients. The TP53 mutation detection rate in children presenting with ACC or choroid plexus carcinomas, and in females with breast cancer before age 31 years, without additional features indicative of LFS, was 45%, 42% and 6%, respectively. The mean age of tumor onset was statistically different (P < .05) between carriers harboring dominant-negative missense mutations (21.3 years) and those with all types of loss of function mutations (28.5 years) or genomic rearrangements (35.8 years). Affected children, except those with ACC, harbored mostly dominant-negative missense mutations. Conclusion The clinical gradient of the germline TP53 mutations, which should be validated by other studies, suggests that it might be appropriate to stratify the clinical management of LFS according to the class of the mutation.


2021 ◽  
Vol 12 ◽  
Author(s):  
Yuan Liu ◽  
Hongke Ding ◽  
Tizhen Yan ◽  
Ling Liu ◽  
Lihua Yu ◽  
...  

PACS1 neurodevelopmental disorder (PACS1-NDD) is a category of rare disorder characterized by intellectual disability, speech delay, dysmorphic facial features, and developmental delay. Other various physical abnormalities of PACS1-NDD might involve all organs and systems. Notably, there were only two unique missense mutations [c.607C &gt; T (p.Arg203Trp) and c.608G &gt; A (p.Arg203Gln)] in PACS1 that had been identified as pathogenic variants for PACS1-NDD or Schuurs-Hoeijmakers syndrome (SHMS). Previous reports suggested that these common missense variants were likely to act through dominant-negative or gain-of-function effects manner. It is still uncertain whether the intragenic deletion or duplication in PACS1 will be disease-causing. By using whole-exome sequencing, we first identified a novel heterozygous multi-exon deletion covering exons 12–24 in PACS1 (NM_018026) in four individuals (two brothers and their father and grandfather) in a three-generation family. The younger brother was referred to our center prenatally and was evaluated before and after the birth. Unlike SHMS, no typical dysmorphic facial features, intellectual problems, and structural brain anomalies were observed among these four individuals. The brothers showed a mild hypermyotonia of their extremities at the age of 3 months old and recovered over time. Mild speech and cognitive delay were also noticed in the two brothers at the age of 13 and 27 months old, respectively. However, their father and grandfather showed normal language and cognitive competence. This study might supplement the spectrum of PACS1-NDD and demonstrates that the loss of function variation in PACS1 displays no contributions to the typical SHMS which is caused by the recurrent c.607C &gt; T (p.Arg203Trp) variant.


Blood ◽  
2019 ◽  
Vol 134 (Supplement_1) ◽  
pp. 2519-2519
Author(s):  
Koichi Ricardo Katsumura ◽  
Peng Liu ◽  
Charu Mehta ◽  
Kyle J Hewitt ◽  
Alexandra Soukup ◽  
...  

The master regulator of hematopoiesis GATA2 controls generation and function of hematopoietic stem and progenitor cells, and heterozygous GATA2 mutations create a predisposition to develop immunodeficiency, myelodysplasia, and acute myeloid leukemia (Spinner et al. Blood, 2014; Dickinson et al. Blood, 2014; Churpek and Bresnick J. Clin. Invest. 2019). Although mechanisms that trigger the transition of a non-pathogenic GATA2 mutation into overt pathology are enigmatic, a paradigm has arisen in which GATA2 mutations are considered to be loss-of-function. We developed a genetic rescue assay to quantify the function of wild type GATA2 and GATA2 disease mutants when expressed at near-physiological levels in primary progenitor cells and demonstrated that GATA2 disease mutations abrogate certain biological and molecular activities, while enabling others (Katsumura et al., 2018, PNAS). We isolated lineage-negative (Lin-) or Lin-Kit+ cells from fetal liver of mice with a homozygous mutation of the Gata2 -77 enhancer, which downregulates Gata2 expression by ~80%. The mutant progenitor cells are largely defective in erythroid, megakaryocytic and granulocytic differentiation and exhibit a predominant monocytic differentiation fate (Johnson et al., 2015, Science Adv.). We compared GATA2 and GATA2 disease mutant activities in the rescue system using a colony formation assay. GATA2, R307W mutant (in N-finger) and T354M mutant (in DNA-binding C-finger) rescued myeloid colony formation and promoted granulocyte proliferation. Surprisingly, R307W and T354M induced more CFU-GM than GATA2. GATA2 and R307W, but not T354M, rescued BFU-E. These data indicated that GATA2 disease mutations were not strictly inhibitory, and in certain contexts, mutant activities exceeded that of GATA2. To extend these results, we subjected -77+/+ or -77-/- Lin- cells to a short-term ex vivo liquid culture, expressed GATA2, R307W, or T354M and used RNA-seq to elucidate progenitor cell transcriptomes. While -77+/+ Lin- cells generate erythroid and myeloid cells, -77-/- Lin- cells are competent for myeloid, but not erythroid, differentiation. Comparison of -77+/+ and -77-/- cell transcriptomes revealed 3064 differentially expressed genes (>2-fold). 1824 genes were >2-fold higher in -77+/+ cells, and 1240 genes were >2-fold higher in -77-/- cells. GATA2 expression in -77-/- cells activated 834 genes >2-fold and repressed 503 genes >2-fold. 60-65% of these genes overlapped with genes differentially expressed between -77+/+ cells and -77-/- cells. R307W expression activated 661 genes >2-fold and repressed 523 genes >2-fold. T354M expression activated 468 genes >2-fold and repressed 575 genes >2-fold. The genes regulated by mutants included GATA2-regulated genes and certain genes that were not GATA2-regulated. Multiple genes were hypersensitive to the mutants, relative to GATA2, and the mutants ectopically regulated certain genes. However, R307W and T354M did not universally regulate an identical gene cohort. For example, both R307W and T354M activated Ncam1, Nrg4, and Mpo more strongly than GATA2. R307W, but not T354M, activated Ear2 and Ces1d more strongly than GATA2. By contrast, T354M, but not R307W, activated Ctsg, Epx, and Rab38 more strongly than GATA2. Both R307W and T354M repressed macrophage genes similarly to GATA2, but they lacked the capacity to activate mast cell genes, differing from GATA2. To elucidate molecular mechanisms underlying GATA2 mutant activities, we leveraged our prior discovery that p38 or ERK kinases induce multi-site GATA2 phosphorylation (Katsumura et al. Blood. 2017). We tested whether these kinases mediate the ectopic transcriptional regulatory activity of GATA2 disease mutants. p38 inhibition attenuated aberrant regulation of Ear2 and Ces1d by R307W (p < 0.05), and mutation of S192 to S192A decreased R307W-induced CFU-GM formation by 49% (p < 0.05). In aggregate, these results indicate that GATA2 disease mutants exert context-dependent activities to regulate transcription and differentiation, activities can be signal-dependent and certain activities are distinct from GATA2. It is attractive to consider the pathogenic consequences of GATA2 disease mutant gain-of-function activities, and an important implication is GATA2 mutation-associated hematologic diseases might not solely reflect haploinsufficiency. Disclosures No relevant conflicts of interest to declare.


Blood ◽  
2020 ◽  
Vol 136 (Supplement 1) ◽  
pp. 1-1
Author(s):  
Tanzir Ahmed ◽  
Tuoen Liu ◽  
Michael O. Alberti ◽  
Brian Wadugu ◽  
Matthew Ndonwi ◽  
...  

Introduction. Mutations in TP53 are common (~18%) in patients with myelodysplastic syndrome (MDS) and acute myeloid leukemia and often undergo loss of heterozygosity. Our understanding of the hematopoietic consequences of expressing mutant TP53-R175H, one of the most common mutations in MDS, is incomplete. In addition, whether TP53-R175H confers a loss-of-function, gain-of-function, or dominant-negative effect in response to chemotherapy has not been fully explored. Methods. We used a constitutive knock-in mouse model expressing TRP53-R172H (G-to-A substitution at nucleotide 515), corresponding to human mutant TP53-R175H. We generated Trp53R172H/+ and Trp53R172H/R172H mice and compared them to wild type (WT), Trp53+/-, and Trp53-/- mice. Peripheral blood (PB) and bone marrow (BM) was analyzed in non-BM transplant conditions, following a non-competitive BM transplant, and following a competitive BM transplant with or without exposure to N-ethyl-N-nitrosourea (ENU) and 5-fluorouracil (5FU). Results. BM hematopoietic stem and progenitor cells (HSPC), including LSK-SLAM cells, were increased in Trp53+/- and Trp53-/-mice (n=4-8, 8-15 weeks old, P&lt;0.01), but not Trp53R172H/+ and Trp53R172H/R172H mice. In order to study the hematopoietic cell-intrinsic properties of mutant TRP53, we transplanted whole BM into lethally irradiated congenic recipient mice and monitored survival. The median overall survival was dependent on the Trp53 genotype of donor cells: WT cells (100% survival at 1 year), Trp53R172H/+ (60% survival at 1 year), Trp53+/- (31 weeks), Trp53-/- (20 weeks), and Trp53R172H/R172H (18 weeks) (n=12-20, P&lt;0.01 for all genotypes vs. WT). To test long-term HSC function of mutant cells, we performed a competitive BM transplant by injecting equal numbers of test and congenic competitor BM into lethally irradiated congenic recipient mice and monitored PB chimerism of recipient mice for 16 weeks. There was PB competitive advantage for all TRP53 mutant cells compared to WT competitor cells, with Trp53-/- cells having the most significant advantage compared to all other mutant genotypes (n=9-11, P&lt;0.05). The results suggest that mutant TRP53-R172H has distinct properties compared to Trp53 deletions, and not consistent with loss-of-function. TP53 mutant cells can clonally expand in patients following cytotoxic chemotherapy. Therefore, we investigated the response of TRP53R172H/+ mutant cells to alkylator (ENU) exposure. We created mixed BM chimeric mice by transplanting test (WT, Trp53+/-, Trp53R172H/+ and Trp53-/-) and WT competitor BM in a 1:3 ratio, respectively. Following engraftment, chimeric mice received vehicle or ENU (2 doses of 100 mg/kg, 9 days apart). ENU-exposed Trp53R172H/+ cells have a robust PB multilineage competitive advantage relative to placebo (Fig. 1A, n = 4-5, 2-fold increase at 10 weeks post-ENU, P&lt;0.001). This expansion was greater than the rise observed for ENU-treated Trp53+/- cells relative to vehicle treatment (1.67-fold relative to vehicle), and similar to the expansion of Trp53-/- cells, regardless of ENU. BM cells from Trp53R172H/+ mice were resistant to ENU-induced p21 expression and cell cycle arrest observed in WT and Trp53+/- mice (n = 4-5, P&lt;0.001, Fig. 1B, C). The results suggest that mutant TRP53-R172H induces a dominant-negative effect following ENU exposure, similar to prior reports following irradiation. Next, we asked whether mutant TRP53-R172H has similar or different effects as Trp53 deletion following exposure to an alternative chemotherapy (5FU). We first treated mice with a single dose of 5FU (200 mg/kg) to deplete cells and monitored WBC count recovery for 4 weeks. Trp53R172H/+ mice had significantly higher recovery WBC counts compared to WT, Trp53+/-, andTrp53-/- mice (n = 5-15, P&lt;0.05, Fig. 1D). Next, we exposed mutant mice to 4 doses of 5FU (150mg/kg x 1 dose, 90 mg/kg x 3 doses, once per week) and monitored survival. We observed that all Trp53-/- mice survived, while Trp53R172H/+ mice had a median survival of 21 days, and Trp53+/- and WT mice had the shortest median survival (13 and 14.5 days, respectively, Fig. 1E). The results suggest that mutant TRP53-R172H cells display a gain-of-function property following a single dose of 5FU. Collectively, the results indicate that mutant TRP53-R172H may induce a gain-of-function or a dominant-negative effect depending on the exposure to specific hematopoietic stresses. Disclosures No relevant conflicts of interest to declare.


Author(s):  
Jiangtao Lei ◽  
mengqiang Cai ◽  
Yun Shen ◽  
Dongdong Lin ◽  
Xiaohua Deng

p53 mutant aggregation can lead to loss-of-function (LoF), dominant-negative (DN) and gain-of-function (GoF) effects, involving in tumor growth. Finding inhibition methods of p53 mutant aggregation is a key step for...


2020 ◽  
Vol 21 (4) ◽  
pp. 1334 ◽  
Author(s):  
Katarzyna A. Roszkowska ◽  
Slawomir Gizinski ◽  
Maria Sady ◽  
Zdzislaw Gajewski ◽  
Maciej B. Olszewski

Forty years of research has proven beyond any doubt that p53 is a key regulator of many aspects of cellular physiology. It is best known for its tumor suppressor function, but it is also a regulator of processes important for maintenance of homeostasis and stress response. Its activity is generally antiproliferative and when the cell is damaged beyond repair or intensely stressed the p53 protein contributes to apoptosis. Given its key role in preventing cancer it is no wonder that it is the most frequently mutated gene in human cancer. Surprisingly, a subset of missense mutations occurring in p53 (gain-of-function) cause it to lose its suppressor activity and acquire new functionalities that turn the tumor suppressor protein into an oncoprotein. A solid body of evidence exists demonstrating increased malignancy of cancers with mutated p53 in all aspects considered “hallmarks of cancer”. In this review, we summarize current findings concerning the cellular processes altered by gain-of-function mutations in p53 and their influence on cancer invasiveness and metastasis. We also present the variety of molecular mechanisms regulating these processes, including microRNA, direct transcriptional regulation, protein–protein interactions, and more.


Author(s):  
Eduardo Alvarado-Ortiz ◽  
Karen Griselda de la Cruz-López ◽  
Jared Becerril-Rico ◽  
Miguel Angel Sarabia-Sánchez ◽  
Elizabeth Ortiz-Sánchez ◽  
...  

Frequent p53 mutations (mutp53) not only abolish tumor suppressor capacities but confer various gain-of-function (GOF) activities that impacts molecules and pathways now regarded as central for tumor development and progression. Although the complete impact of GOF is still far from being fully understood, the effects on proliferation, migration, metabolic reprogramming, and immune evasion, among others, certainly constitute major driving forces for human tumors harboring them. In this review we discuss major molecular mechanisms driven by mutp53 GOF. We present novel mechanistic insights on their effects over key functional molecules and processes involved in cancer. We analyze new mechanistic insights impacting processes such as immune system evasion, metabolic reprogramming, and stemness. In particular, the increased lipogenic activity through the mevalonate pathway (MVA) and the alteration of metabolic homeostasis due to interactions between mutp53 and AMP-activated protein kinase (AMPK) and Sterol regulatory element-binding protein 1 (SREBP1) that impact anabolic pathways and favor metabolic reprograming. We address, in detail, the impact of mutp53 over metabolic reprogramming and the Warburg effect observed in cancer cells as a consequence, not only of loss-of-function of p53, but rather as an effect of GOF that is crucial for the imbalance between glycolysis and oxidative phosphorylation. Additionally, transcriptional activation of new targets, resulting from interaction of mutp53 with NF-kB, HIF-1α, or SREBP1, are presented and discussed. Finally, we discuss perspectives for targeting molecules and pathways involved in chemo-resistance of tumor cells resulting from mutp53 GOF. We discuss and stress the fact that the status of p53 currently constitutes one of the most relevant criteria to understand the role of autophagy as a survival mechanism in cancer, and propose new therapeutic approaches that could promote the reduction of GOF effects exercised by mutp53 in cancer.


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