Hypomorphic RAG deficiency: impact of disease burden on survival and thymic recovery argues for early diagnosis and HSCT.

Patients with hypomorphic mutations in the RAG1 or RAG2 gene present with either Omenn syndrome or atypical combined immunodeficiency with a wide phenotypic range. Hematopoietic stem cell transplantation (HSCT) is potentially curative, but data are scarce. We report on a worldwide cohort of 60 patients with hypomorphic RAG variants who underwent HSCT, 78% of whom experienced infections (29% active at HSCT), 72% had autoimmunity, and 18% had granulomas pretransplant. These complications are frequently associated with organ damage. Eight individuals (13%) were diagnosed by newborn screening or family history. HSCT was performed at a median of 3.4 years (range 0.3-42.9 years) from matched unrelated donors, matched sibling or matched family donors, or mismatched donors in 48%, 22%, and 30% of the patients, respectively. Grafts were T-cell depleted in 15 cases (25%). Overall survival at 1 and 4 years was 77.5% and 67.5% (median follow-up of 39 months). Infection was the main cause of death. In univariable analysis, active infection, organ damage pre-HSCT, T-cell depletion of the graft, and transplant from a mismatched family donor were predictive of worse outcome, whereas organ damage and T-cell depletion remained significant in multivariable analysis (hazard ratio [HR] = 6.01, HR = 8.46, respectively). All patients diagnosed by newborn screening or family history survived. Cumulative incidences of acute and chronic graft-versus-host disease were 35% and 22%, respectively. Cumulative incidences of new-onset autoimmunity was 15%. Immune reconstitution, particularly recovery of naïve CD4+ T cells, was faster and more robust in patients transplanted before 3.5 years of age, and without organ damage. These findings support the indication for early transplantation.

Beluga whale and bottlenose dolphin ACE2 proteins allow cell entry mediated by spike protein from three variants of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) viruses infect numerous non-human species. Spillover of SARS-CoV-2 into novel animal reservoirs may present a danger to host individuals of these species, particularly worrisome in populations already endangered or threatened by extinction. In addition, emergence in new reservoirs could pose spillback threats to humans, especially in the form of virus variants that further mutate when infecting other animal hosts. Previous work suggests beluga whales (Delphinapterus leucas) and bottlenose dolphins (Tursiops truncatus) may be at risk owing to their formation of social groups, contact with humans, exposure to contaminated wastewater, and structure of their angiotensin-converting enzyme 2 (ACE2) proteins, which SARS-CoV-2 uses as a cellular receptor. We examined marine-mammal susceptibility to virus infection by challenging 293T cells expressing beluga or dolphin ACE2 with pseudovirions bearing the SARS-CoV-2 spike protein. Beluga and dolphin ACE2 were sufficient to allow cell entry by an early pandemic isolate (Wuhan-Hu-1) and two evolved variants (Delta B.1.617.2 and Omicron BA.1 strains). We conclude that SARS-CoV-2 poses a potential threat to marine mammal reservoirs that should be considered in surveillance efforts.

Identification of four novel variant in the AMHR2 gene in six unrelated Turkish families.

PURPOSE: Persistent Müllerian duct syndrome (PMDS) is characterized by the persistence of Müllerian structures in male with normal phenotype. Most cases occur as a result of mutations in the anti-Müllerian hormone (AMH) or AMHR2 genes. In this study, we aim to discuss the results of clinical, laboratory, and molecular genetic analysis of cases detected to have AMHR2 gene mutation. METHODS: A total of 11 cases from 6 families were included in the study. AMHR2 gene mutation analyses were performed by sequencing of the coding exons and the exon-intron boundaries of the genes. The American College of Medical Genetics guidelines were used for the classification of the detected variants. RESULTS: Six of the 11 cases were admitted due to bilateral undescended testes and five cases due to inguinal hernia (three transverse testicular ectopia and two hernia uterus inguinalis). All cases had normal AMH levels. Seven different variants were identified in the six families. The variants detected in four cases were considered novel (c.78del, c.71G > A, c.1460dup, c.1319A > G). Two of the novel variants were missense (exon 2 and exon 10) mutations, one was deletion (exon 2), and one duplication (exon 11). CONCLUSION: We identified four novel mutations in the AMHR2 gene resulting in PMDS. Duplication mutation (c.1460dup) in the AMHR2 gene causing PMDS was demonstrated for the first time. The most important complications of PMDS are infertility and malignancy. Early diagnosis is vital to preventing malignancy. Vas deferens and vascular structures may be injured during orchiopexy. Therefore, patients should always be referred to experienced clinics.

A DIFFERENT PERSPECTIVE OF ELEVATED LACTATE IN PEDIATRIC PATIENTS WITH DIABETIC KETOACIDOSIS.

OBJECTIVE: This study aims to determine the frequency and prognostic significance of lactic acidosis in children with diabetic ketoacidosis (DKA) admitted to the pediatric intensive care unit. METHODS: The study was carried out retrospectively by examining the patients admitted to the pediatric intensive care unit for the treatment of DKA. The ages of the patients ranged from 2 to 18 years. The patients with the following parameters were enrolled in the study: serum blood glucose>200 mg/dL, ketonuria presence, venous blood gas pH ≤7.1, bicarbonate <15. RESULTS: A total of 56 patients were included in the study with a mean age of 111.07 ± 51.13 months. The recovery time from DKA was 16.05 ± 6.25 h in the group with low lactate level and it was 13.57 ± 8.34 h in the group with high lactate level with no statistically significant difference. There was a negative correlation between lactate levels and the recovery time from DKA. CONCLUSION: Lactic acidosis is common in DKA, and unlike other conditions, such as sepsis, it is not always a finding of poor prognosis that predicts the severity of the disease or mortality. We think that high lactate may even protect against possible brain edema-cerebral damage in DKA.

In utero effects of maternal phthalate exposure on male genital development.

BACKGROUND: Phthalates are used extensively in commercial and personal care products and maternal exposure is ubiquitous. Phthalates are anti-androgenic, but the potential effects of phthalates on male penile development have not been assessed in utero. OBJECTIVE: The study aims to investigate the association between early pregnancy phthalate exposure and fetal penile development, overall and by race. METHODS: Prospective cohort study of women with singleton pregnancies presenting for prenatal ultrasound between 18 and 22 weeks' gestation. Maternal urine samples were assayed for eight phthalate monoester metabolites. We used maternal phthalate levels at 18 to 22 weeks' gestation as predictors of fetal size using multiple linear regression models, adjusted for fetal gestational age, maternal age, race, smoking, and education. We incorporated a phthalate by race interaction into a second set of regression models. RESULTS: We detected statistically significant race interactions for continuous phthalates with penile width. Race interactions were also suggested for penile length and volume using tertiles of phthalates with point estimates generally positive for whites and negative for African Americans. CONCLUSION: Penile development is significantly influenced by race, and the impact of maternal phthalates on penile measurements also varies by race. Maternal phthalate exposure can adversely affect in utero penile growth and development, especially among African Americans.

Genotype-phenotype correlation, gonadal malignancy risk, gender preference, and testosterone/dihydrotestosterone ratio in steroid 5-alpha-reductase type 2 deficiency: a multicenter study from Turkey.

BACKGROUND: Studies regarding genetic and clinical characteristics, gender preference, and gonadal malignancy rates for steroid 5-alpha-reductase type 2 deficiency (5α-RD2) are limited and they were conducted on small number of patients. OBJECTIVE: To present genotype-phenotype correlation, gonadal malignancy risk, gender preference, and diagnostic sensitivity of serum testosterone/dihydrotestosterone (T/DHT) ratio in patients with 5α-RD2. MATERIALS AND METHODS: Patients with variations in the SRD5A2 gene were included in the study. Demographic characteristics, phenotype, gender assignment, hormonal tests, molecular genetic data, and presence of gonadal malignancy were evaluated. RESULTS: A total of 85 patients were included in the study. Abnormality of the external genitalia was the most dominant phenotype (92.9%). Gender assignment was male in 58.8% and female in 29.4% of the patients, while it was uncertain for 11.8%. Fourteen patients underwent bilateral gonadectomy, and no gonadal malignancy was detected. The most frequent pathogenic variants were p.Ala65Pro (30.6%), p.Leu55Gln (16.5%), and p.Gly196Ser (15.3%). The p.Ala65Pro and p.Leu55Gln showed more undervirilization than the p.Gly196Ser. The diagnostic sensitivity of stimulated T/DHT ratio was higher than baseline serum T/DHT ratio, even in pubertal patients. The cut-off values yielding the best sensitivity for stimulated T/DHT ratio were ≥ 8.5 for minipuberty, ≥ 10 for prepuberty, and ≥ 17 for puberty. CONCLUSION: There is no significant genotype-phenotype correlation in 5α-RD2. Gonadal malignancy risk seems to be low. If genetic analysis is not available at the time of diagnosis, stimulated T/DHT ratio can be useful, especially if different cut-off values are utilized in accordance with the pubertal status.

Systems level expression correlation of Ras GTPase regulators.

BACKGROUND: Proteins of the ubiquitously expressed core proteome are quantitatively correlated across multiple eukaryotic species. In addition, it was found that many protein paralogues exhibit expression anticorrelation, suggesting that the total level of protein with a given functionality must be kept constant. METHODS: We performed Spearman's rank correlation analyses of gene expression levels for the RAS GTPase subfamily and their regulatory GEF and GAP proteins across tissues and across individuals for each tissue. A large set of published data for normal tissues from a wide range of species, human cancer tissues and human cell lines was analysed. RESULTS: We show that although the multidomain regulatory proteins of Ras GTPases exhibit considerable tissue and individual gene expression variability, their total amounts are balanced in normal tissues. In a given tissue, the sum of activating (GEFs) and deactivating (GAPs) domains of Ras GTPases can vary considerably, but each person has balanced GEF and GAP levels. This balance is impaired in cell lines and in cancer tissues for some individuals. CONCLUSIONS: Our results are relevant for critical considerations of knock out experiments, where functionally related homologs may compensate for the down regulation of a protein.

Duncan's dermatosis: from the "terra firma-forme" to a possible syndromic condition. The story of a dirty disease.

Since its first description by Duncan, Tschen and Knox in 1987 in the former Archives of Dermatology (1), "Terra firma-forme dermatosis" has been variously described in medical literature, representing a strange, probably underestimated, cutaneous disease. During the last 40 years, the condition has been recorded as an undesirable as well as unexplained event, occurring mainly in childhood, characterized by a brownish-black appearance of the whole skin, resembling dirt. Recently, authors described several cases of atypical patterns of the disease, sometimes with impressing topographic clinical pictures, evocative for syndromic phenotypes. Thanks to more careful examination of the tegument, often with the aid of non-invasive diagnostic tools, attention to this disease is growing. This brief review summarizes the state of the art on the topic, through an historical overview of what is known of this 'dirty' dermatosis.

Defining a minimal cell: essentiality of small ORFs and ncRNAs in a genome-reduced bacterium.

Identifying all essential genomic components is critical for the assembly of minimal artificial life. In the genome-reduced bacterium Mycoplasma pneumoniae, we found that small ORFs (smORFs; < 100 residues), accounting for 10% of all ORFs, are the most frequently essential genomic components (53%), followed by conventional ORFs (49%). Essentiality of smORFs may be explained by their function as members of protein and/or DNA/RNA complexes. In larger proteins, essentiality applied to individual domains and not entire proteins, a notion we could confirm by expression of truncated domains. The fraction of essential non-coding RNAs (ncRNAs) non-overlapping with essential genes is 5% higher than of non-transcribed regions (0.9%), pointing to the important functions of the former. We found that the minimal essential genome is comprised of 33% (269,410 bp) of the M. pneumoniae genome. Our data highlight an unexpected hidden layer of smORFs with essential functions, as well as non-coding regions, thus changing the focus when aiming to define the minimal essential genome.

CLINICAL FEATURES AND GENETIC ANALYSIS OF SIX PATIENTS WITH WISKOTT-ALDRICH SYNDROME REPORTING TWO NOVEL MUTATIONS: EXPERIENCE OF ERCIYES UNIVERSITY, KAYSERI, TURKEY.

AIM: The Wiskott-Aldrich syndrome (WAS) is an X-linked immunodeficiency characterized by micro-thrombocytopenia, eczema, and recurrent infections. We aimed to share our experience with six children with WAS, including two patients with two novel mutations. MATERIAL AND METHOD: We present phenotypical and laboratory description of six patients with WAS. The initial clinical presentation, biochemical and radiological features, molecular diagnosis together with long-term follow-up data are provided. RESULTS: The patients showed increased serum levels of IgE; otherwise the serum levels of IgM were decreased. The percentages of CD3+ T cells were decreased or within lower limit. Four patients underwent molecular genetics analysis and Western blot studies; two of them showed unpublished mutations: a hemizygous splice site mutation in intron 8 (c.778-2A>T), and a hemizygous deletion in exon10 of the WASP gene (c.1017delT; p.S339fsX444) were detected. Western blot studies confirmed the reduced WAS protein expression in peripheral mononuclear blood cells in four studied patients. CONCLUSIONS: The major characteristics of patients were thrombocytopenia with decreased mean platelet volume and bleeding. All patients had been previously misdiagnosed as idiopathic thrombocytopenic purpura, demonstrating the importance of a careful differential diagnosis, and intense evaluation.

PARTIAL OCULOCUTANEOUS ALBINISM AND IMMUNODEFICIENCY SYNDROMES: TEN YEARS EXPERIENCE FROM A SINGLE CENTER IN TURKEY.

BACKGROUND AND AIM: Partial oculocutaneous albinism and immunodeficiency (OCA-ID) diseases are autosomal recessive syndromes characterized by partial hypopigmentation and recurrent infections. Moreover, some OCA-ID syndromes confer susceptibility to develop a life-threatening hyperinflammatory condition called hemophagocytic lymphohistiocytosis (HLH). We investigated the genetic, clinical and immunological characteristics of 20 OCA patients. MATERIAL AND METHODS: Herein, we present the clinical and immunological characteristics of 20 OCA patients who referred to the Department of Pediatric Immunology, Erciyes University Medical Faculty in Kayseri, Turkey between 2004 and 2014. RESULTS: Of the 20 OCA patients, 7 fulfilled diagnostic criteria for HLH, 9 showed defective functions of CD8 T cells and natural killer cells, and 8 received a definitive molecular diagnosis. Among the patients, we also report a patient diagnosed with two different genetic defects, in TYR and JAK3 genes, causing, respectively, OCA and ID. CONCLUSION: Our results illustrate the variability of clinical presentations and disease severity in OCA-ID patients, with consequent challenges in diagnosing and treating these patients.

Hematological predictors and clinical outcomes in cardiac surgery.

PURPOSE: The present study was to investigate if five values that are part of the hemogram analysis routinely checked before heart surgeries can be used as a high-quality, quick, low-cost, and easy-to-use outcome predictor. METHODS: This investigation was a retrospective, observational, cross-sectional study. Univariate and multivariate logistic regression was used to identify independent predictors for combined adverse events. We enrolled 1500 consecutive patients who underwent elective, on-pump, open-heart surgery from 2011 to 2014. Preoperative hemogram evaluation, red cell distribution width (RDW), mean platelet volume (MPV), platelet-to-lymphocyte ratio (PLR), and neutrophil-to-lymphocyte ratio (NLR) were recorded. We classified combined adverse events (CAE) as (1) myocardial infarction, (2) cardiac reoperation, (3) prolonged mechanical ventilation, (4) prolonged hospital stay, (5) rehospitalization, or (6) mortality. RESULTS: It was found that several parameters obtained as part of the hemogram, namely RDW, MPV, PLR, and NLR, can predict, individually or in combinations, the outcomes in open-heart surgery patients. It was found that the prediction success of NLR (4.8 fold) was higher compared to RDW (1.8 fold) and MPV (1.5 fold). When the prediction success of the combined parameters was investigated, the NLR-RDW (4.7 fold) pair was found higher in the prediction of CAE occurrence. The predictive success of the triple combination of NLR-MPV-RDW (5.5 fold) was higher than other combinations. CONCLUSIONS: The triple combination of parameters obtained as part of the hemogram, NLR-RDW-MPV, indicated a much more predictive power than two parameters coupled. This combination of three parameters, NLR-RDW-MPV, is to be considered as a sensitive, high-quality, low-cost outcome prediction marker for cardiac surgery patients that is less time consuming and easy to use.

Effect of anti-smoking advertisements on Turkish adolescents.

The aim of the present study was to determine the perception of 10 anti-smoking advertisements in 1434 Turkish adolescents. We used the Effectiveness of the Anti-smoking Advertisements Scale, which included 6 items for each advertisement; each item was assessed on a 5-point Likert-type scale. Multiple logistic regression analysis was used to determine the factors associated with the impact of the advertisements. All the advertisements were more effective for adolescents who had never smoked compared to ex-smokers and current smokers. We also noted that, regardless of age, smoking status decreased the effectiveness of all the advertisements. Previous studies have shown that smokers have a negative attitude towards anti-smoking messages. In the present study, the most effective advertisements among adolescents were those with "Sponge and tar", "Smoking harms in every breath" and "Children want to grow". In conclusion, although anti-smoking campaigns are targeted towards adults, they also have a strong influence on adolescents. The main target population for advertisements should be individuals aged < 15 years who have not yet started smoking.

Maternal inflammatory markers and term labor performance.

OBJECTIVE: We sought to examine the relationship between maternal markers of inflammation and labor performance. STUDY DESIGN: A nested cohort study was performed utilizing an established cohort of term nulliparous patients. Maternal blood was collected at the onset of regular, painful contractions in patients undergoing labor induction or at admission in patients with spontaneous labor. Levels of cytokines including interleukin (IL)-1, IL-6, and tumor necrosis factor-α were determined using standard multiplex methodology. Maternal demographic data were collected prospectively. Detailed retrospective chart review was performed to extract data on cervical dilation, effacement, and station during labor. Subjects were excluded if they failed to achieve complete dilation. Mixed effects modeling was used to examine the association between serum cytokine quartiles and labor progress in the latent and active phases. RESULTS: In all, 334 women were included in our analysis. The lowest quartile of IL-6 was associated with slower latent labor (P = .001). In contrast, the highest quartiles of IL-1 and tumor necrosis factor-α were associated with slower active labor (P = .03 and .0002, respectively). CONCLUSION: Proinflammatory activation is important in labor initiation. However, once active labor is established, excess inflammation can be detrimental to efficient labor progress. These data may explain, in part, the known associations among clinical chorioamnionitis, cesarean delivery, and postpartum hemorrhage.

Severe congenital neutropenia in two siblings related to HAX1 mutation without neurodevelopmental disorders.

Severe congenital neutropenia (SCN) is a rare primary myelopoiesis disorder, characterized by reduced absolute neutrophil counts from birth, increased susceptibility to recurrent and life-threatening infections, and a preleukemic predisposition. Herein, we describe two siblings with SCN born from consanguineous parents who were referred for complaints of recurrent cutaneous infections, gingivitis, purulent otitis media, and both lower and upper respiratory tract infections. Bone marrow aspiration of one patient demonstrated a maturation arrest in the myeloid lineage at the promyelocyte-myelocyte stages. Genetic analysis revealed a homozygous mutation in exon 2 c.130-131insA; p.W44X in the HAX1 gene. Although identical mutations were detected in both siblings, there was a clear discrepancy between the clinical course of the brother, who eventually required granulocyte colony stimulating factor (G-CSF) therapy, and the sister, who did not. Although SCN is a rare disorder, the early onset of recurrent infections and severe neutropenia, especially in children born from consanguineous parents, should always raise suspicion and warrant further evaluation.

The clinical features and genetic mutations of chronic granulomatous disease: results from a reference centre at middle Anatolia.

AIM: Chronic granulomatous disease (CGD) is a rare innate immune deficiency with neutrophil function disorder. In this retrospective study, we aimed to evaluate the clinical features of the patients with CGD. MATERIAL AND METHOD: We presented eight patients (6 boys, 2 girls) with CGD which were evaluated at Erciyes University Medical Faculty hospital between 1996 and 2012. The initial complaints, age at diagnosis, consanguinity of the parents, similar disease history or death of the siblings, physical examination, diagnostic tests, clinical courses, and genetic characteristics were analyzed. RESULTS: The initial complaints were started before the age of one in four patients; whereas only two patients diagnosed before the first birth day. Lymphadenomegally, suppurative infections, pneumonia, diarrhea were the most noted initial complaints. All parents were consanguineous. The clinical features were mild; and the ages of diagnosis were late in patients with p47 and p67 defect. The patient with X linked CGD was diagnosed when he was 3 months old; his clinical course was complicated with chronic otitis media, zygomatic abscess, lung abscess, and facial paralysis. The patient with p22 defect was diagnosed at two months of age; and gastric wall granuloma, inflammation in proximal femur was detected. CONCLUSIONS: The awareness of the clinicians about CGD will result in early diagnosis and consequently reduce the mortality and morbidity of this disease.

Chylothorax due to thrombosis of the jugular and subclavian veins in a patient with gastric cancer: a case report.

BACKGROUND: Chylothorax is a rare condition due to leakage of chyle in the thoracic cavity. When large amounts of chyle leak into the thoracic cavity, it can lead to severe respiratory, immune, and metabolic complications. Chylothorax has many potential underlying etiologies, and the most common causes are traumatic chylothorax and lymphoma. Venous thrombosis of the upper extremities is a rare cause of a chylothorax. CASE PRESENTATION: A 62-year-old Dutch man with a medical history of gastric cancer, treated with neoadjuvant chemotherapy and surgery 13 months prior, presented with dyspnea and a swollen left arm. Computed tomography thorax showed bilateral pleural effusion that was more prominent on the left side. The computed tomography scan further revealed thrombosis of the left jugular and subclavian veins and osseal masses suggesting cancer metastasis. Thoracentesis was performed to confirm the suspicion of gastric cancer metastasis. The obtained fluid was milky with a high level of triglycerides, but contained no malignant cells; hence, the diagnosis of the pleural effusion was chylothorax. Treatment with anticoagulation and a medium-chain-triglycerides diet was started. Furthermore, bone metastasis was confirmed with a bone biopsy. CONCLUSION: Our case report demonstrates chylothorax as a rare cause of dyspnea in a patient with pleural effusion and a history of cancer. Therefore, this diagnosis should be considered in all patients with a history of cancer with new-onset pleural effusion and thrombosis of the upper extremities or clavicular/mediastinal lymphadenopathy.

Texture features of primary tumor on 18F-FDG PET images in non-small cell lung cancer: The relationship between imaging and histopathological parameters. / Características de textura del tumor primario en imágenes de 18F-FDG PET en cáncer de pulmón de células no pequeñas: la relación entre parámetros de imágenes y parámetros histopatológicos.

OBJECTIVES: The aims of this study were to evaluate the relationships between textural features of the primary tumor on FDG PET images and clinical-histopathological parameters which are useful in predicting prognosis in newly diagnosed non-small cell lung cancer (NSCLC) patients. MATERIAL AND METHODS: PET/CT images of ninety (90) patients with NSCLC prior to surgery were analyzed retrospectively. All patients had resectable tumors. From the images we acquired data related to metabolism (SUVmax, metabolic tumor volume [MTV] and total lesion glycolysis [TLG]) and texture features of primary tumors. Histopathological tumor types and subgroups, degree of Ki-67 expression and necrosis rates of the primary tumor, mediastinal lymph node (MLN) status and nodal stages were recorded. RESULTS: Among the 2histologic tumor types (adenocarcinoma and squamous cell carcinoma) significant differences were present regarding metabolic parameters, Ki-67 index with higher values and kurtosis with lower values in the latter group. Textural heterogeneity was found to be higher in poorly differentiated tumors compared to moderately differentiated tumors in patients with adenocarcinoma. While Ki-67 index had significant correlations with metabolic parameters and kurtosis, tumor necrosis rate was only significantly correlated with textural features. By univariate and multivariate analyses of the imaging and histopathological factors examined, only gradient variance was significant predictive factor for the presence of MLN metastasis. CONCLUSIONS: Textural features had significant associations with histologic tumor types, degree of pathological differentiation, tumor proliferation and necrosis rates. Texture analysis has potential to differentiate tumor types and subtypes and to predict MLN metastasis in patients with NSCLC.

A RAC-GEF network critical for early intestinal tumourigenesis.

RAC1 activity is critical for intestinal homeostasis, and is required for hyperproliferation driven by loss of the tumour suppressor gene Apc in the murine intestine. To avoid the impact of direct targeting upon homeostasis, we reasoned that indirect targeting of RAC1 via RAC-GEFs might be effective. Transcriptional profiling of Apc deficient intestinal tissue identified Vav3 and Tiam1 as key targets. Deletion of these indicated that while TIAM1 deficiency could suppress Apc-driven hyperproliferation, it had no impact upon tumourigenesis, while VAV3 deficiency had no effect. Intriguingly, deletion of either gene resulted in upregulation of Vav2, with subsequent targeting of all three (Vav2-/- Vav3-/- Tiam1-/-), profoundly suppressing hyperproliferation, tumourigenesis and RAC1 activity, without impacting normal homeostasis. Critically, the observed RAC-GEF dependency was negated by oncogenic KRAS mutation. Together, these data demonstrate that while targeting RAC-GEF molecules may have therapeutic impact at early stages, this benefit may be lost in late stage disease.

Conformational energies and entropies of peptides, and the peptide-protein binding problem.

A novel statistical thermodynamic approach is applied to free-peptide segments in order to classify them according to their conformational energies, entropies and heat capacities. Our approach employs the rotational isomeric state (RIS) model in which the states are described by the Ramachandran map of backbone torsion angles. The statistical weight matrices for the pairwise-dependent states are derived from the torsion angle probabilities of the consecutive dipeptides in a coil library. The partition function is determined for a given sequence via RIS multiplication of the pre-determined matrices. The conformational partition function, Helmholtz free energy, energy, entropy and heat capacity are obtained. The model is applied to randomly produced peptides and also to known peptide inhibitors to analyze their thermodynamic properties. Peptides with low energy, low entropy and low-heat capacity are determined to be essential for a peptide to be a good candidate inhibitor. Free energy changes in peptide binding are also discussed.