CAGI SickKids challenges: Assessment of phenotype and variant predictions derived from clinical and genomic data of children with undiagnosed diseases.

Whole-genome sequencing (WGS) holds great potential as a diagnostic test. However, the majority of patients currently undergoing WGS lack a molecular diagnosis, largely due to the vast number of undiscovered disease genes and our inability to assess the pathogenicity of most genomic variants. The CAGI SickKids challenges attempted to address this knowledge gap by assessing state-of-the-art methods for clinical phenotype prediction from genomes. CAGI4 and CAGI5 participants were provided with WGS data and clinical descriptions of 25 and 24 undiagnosed patients from the SickKids Genome Clinic Project, respectively. Predictors were asked to identify primary and secondary causal variants. In addition, for CAGI5, groups had to match each genome to one of three disorder categories (neurologic, ophthalmologic, and connective), and separately to each patient. The performance of matching genomes to categories was no better than random but two groups performed significantly better than chance in matching genomes to patients. Two of the ten variants proposed by two groups in CAGI4 were deemed to be diagnostic, and several proposed pathogenic variants in CAGI5 are good candidates for phenotype expansion. We discuss implications for improving in silico assessment of genomic variants and identifying new disease genes.

Dnmt3a deletion cooperates with the Flt3/ITD mutation to drive leukemogenesis in a murine model.

Internal tandem duplications of the juxtamembrane domain of FLT3 (FLT3/ITD) are among the most common mutations in Acute Myeloid Leukemia (AML). Resulting in constitutive activation of the kinase, FLT3/ITD portends a particularly poor prognosis, with reduced overall survival and increased rates of relapse. We previously generated a knock-in mouse, harboring an internal tandem duplication at the endogenous Flt3 locus, which develops a fatal myeloproliferative neoplasm (MPN), but fails to develop acute leukemia, suggesting additional mutations are necessary for transformation. To investigate the potential cooperativity of FLT3/ITD and mutant DNMT3A, we bred a conditional Dnmt3a knockout to a substrain of our Flt3/ITD knock-in mice, and found deletion of Dnmt3a significantly reduced median survival of Flt3ITD/+ mice in a dose dependent manner. As expected, pIpC treated Flt3ITD/+ mice solely developed MPN, while Flt3ITD/+;Dnmt3af/f and Flt3ITD/+;Dnmt3af/+ developed a spectrum of neoplasms, including MPN, T-ALL, and AML. Functionally, FLT3/ITD and DNMT3A deletion cooperate to expand LT-HSCs, which exhibit enhanced self-renewal in serial re-plating assays. These results illustrate that DNMT3A loss cooperates with FLT3/ITD to generate hematopoietic neoplasms, including AML. In combination with FLT3/ITD, homozygous Dnmt3a knock-out results in reduced time to disease onset, LT-HSC expansion, and a higher incidence of T-ALL compared with loss of just one allele. The co-occurrence of FLT3 and DNMT3A mutations in AML, as well as subsets of T-ALL, suggests the Flt3ITD/+;Dnmt3af/f model may serve as a valuable resource for delineating effective therapeutic strategies in two clinically relevant contexts.

Increased Skin Tumor Incidence and Keratinocyte Hyper-Proliferation in a Mouse Model of Down Syndrome.

Down syndrome (DS) is a genetic disorder caused by the presence of an extra copy of human chromosome 21 (Hsa21). People with DS display multiple clinical traits as a result of the dosage imbalance of several hundred genes. While many outcomes of trisomy are deleterious, epidemiological studies have shown a significant risk reduction for most solid tumors in DS. Reduced tumor incidence has also been demonstrated in functional studies using trisomic DS mouse models. Therefore, it was interesting to find that Ts1Rhr trisomic mice developed more papillomas than did their euploid littermates in a DMBA-TPA chemical carcinogenesis paradigm. Papillomas in Ts1Rhr mice also proliferated faster. The increased proliferation was likely caused by a stronger response of trisomy to TPA induction. Treatment with TPA caused hyperkeratosis to a greater degree in Ts1Rhr mice than in euploid, reminiscent of hyperkeratosis seen in people with DS. Cultured trisomic keratinocytes also showed increased TPA-induced proliferation compared to euploid controls. These outcomes suggest that altered gene expression in trisomy could elevate a proliferation signalling pathway. Gene expression analysis of cultured keratinocytes revealed upregulation of several trisomic and disomic genes may contribute to this hyperproliferation. The contributions of these genes to hyper-proliferation were further validated in a siRNA knockdown experiment. The unexpected findings reported here add a new aspect to our understanding of tumorigenesis with clinical implications for DS and demonstrates the complexity of the tumor repression phenotype in this frequent condition.

Genomic alterations in myeloid neoplasms with novel, apparently balanced translocations.

Characterization of gross chromosomal rearrangements, particularly translocations in neoplasms, has proven to be valuable in patient management by aiding in diagnosis, defining prognosis, and leading to new therapeutic interventions. In this report, we investigate two apparently balanced translocations, t(6;17)(q23.3;p13.3) and t(2;13)(p21;q14.11), in patients with myeloid neoplasms and uncover concomitant microdeletions associated with the breakpoints. Breakpoint mapping by fluorescence in situ hybridization (FISH) detected deletions at or adjacent to all breakpoints. Subsequently, array comparative genomic hybridization on the 244 K Agilent platform refined the deletion boundaries, revealing a 1.7 Mb deletion directly adjacent to the 6q23.3 breakpoint, and a 562 kb deletion at 17p13.3 in the first case. The second case was found to harbor a 195 kb deletion at 2p21 and a 1.4 Mb deletion distal to the 13q breakpoint at 13q14.3. Additionally, a 133 kb deletion within the breakpoint region at 13q14.11 and a 265 kb deletion proximal to the breakpoint were discovered, neither of which was detected by FISH. Although a gene fusion resulting from either novel rearrangement cannot be determined from these data, formation of a fusion transcript cannot be excluded because the resolution of the techniques used does not allow definite delineation of the breakpoint locations. Although the incidence and clinical relevance of these focal imbalances remains to be evaluated, the cases presented here support high resolution evaluation of presumably balanced rearrangements in neoplasms. Such imbalances may portend important hitherto unrecognized prognostic and diagnostic categories.

Novel SSBP2-JAK2 fusion gene resulting from a t(5;9)(q14.1;p24.1) in pre-B acute lymphocytic leukemia.

Activating mutations in JAK2 are found in virtually all patients with polycythemia vera, and about half of those with essential thrombocythemia and primary myelofibrosis. In addition, less common aberrations (particularly gene fusions) involving JAK2 have been described in acute leukemias. With the advent of JAK2 inhibitor trials in myeloproliferative disorders, tumors with JAK2 mutations or rearrangements have become candidates for targeted therapy. In this report, we identify SSBP2 as a new JAK2 fusion partner in a patient with pre-B cell acute lymphocytic leukemia. This finding adds to the expanding compendium of JAK2 aberrations found in various hematopoietic malignancies, as well as the potential need for a diagnostic FISH analysis in the appropriate clinical setting.

Bupropion SR for the treatment of postpartum depression: a pilot study.

Despite the prevalence of postpartum depression, few studies have assessed the efficacy of antidepressants for the treatment of this disorder. Failure to treat postpartum depression (PPD) places the woman at risk for chronic depression and may have adverse effects on child wellbeing and development. Eight female outpatients aged 18-45 yr were enrolled in an 8-wk open-label trial of bupropion SR for PPD. All patients met DSM-IV criteria for major depression with onset within 3 months of delivery and scored 17 or greater on the Hamilton Depression Rating Scale (HAMD) at baseline. Those with onset of depressive symptoms during pregnancy, psychotic symptoms, or significant medical illness were excluded. Median scores on the HAMD declined from 20.5 (range 15-38) at baseline to 10.0 (range 1-20) at end-point (p<0.05, Wilcoxon signed-ranks test; LOCF). Six out of the eight subjects demonstrated a > or =50% decrease in HAMD scores from baseline; three subjects achieved remission (HAMD score of < or =7) at week 8. Median final dosage of bupropion SR was 262.5 (range 37.5-300). Bupropion SR was well tolerated, and no subjects discontinued treatment as a result of medication side-effects. Bupropion SR represents an effective and well-tolerated antidepressant for the treatment of PPD.

Short-term use of estradiol for depression in perimenopausal and postmenopausal women: a preliminary report.

OBJECTIVE: The authors examined the effect of a 4-week course of estrogen therapy on depression in perimenopausal and postmenopausal women. METHOD: Twenty-two depressed women who were either perimenopausal (N=10) or postmenopausal (N=12) received open-label treatment with transdermal 17beta-estradiol (100 micro g/day) for 4 weeks. The Montgomery-Asberg Depression Rating Scale and the Beck Depression Inventory were used to assess depressive symptoms, the Greene Climacteric Scale was used to assess menopause-related symptoms, and the Clinical Global Impression (CGI) was used to assess global clinical improvement in these women at baseline and after treatment. Remission of depression was defined as a score <10 on the Montgomery-Asberg Depression Rating Scale and a score

Efficacy of citalopram as a monotherapy or as an adjunctive treatment to estrogen therapy for perimenopausal and postmenopausal women with depression and vasomotor symptoms.

BACKGROUND: Women frequently report depressive and vasomotor symptoms during the menopausal transition. Hormone therapy has been shown to improve some of these symptoms, although its safety as a long-term treatment has been questioned. It is still unclear whether the use of antidepressants alone may alleviate menopause-related mood and vasomotor symptoms or enhance the response observed with short-term use of estrogen therapy. METHOD: Perimenopausal and postmenopausal women with depressive disorders (DSM-IV criteria) and menopause-related symptoms received treatment with 20 to 60 mg/day of citalopram alone (N = 22) or adjunctive to estrogen therapy (N = 13). Adjunctive treatment was offered to subjects who had failed to show remission of depression after 4 weeks with estrogen therapy (estradiol [E(2)]) alone. Depressive symptoms, menopause-related symptoms, and global clinical improvement were assessed at baseline and at endpoint of adjunctive treatment (8 weeks) or citalopram monotherapy (12 weeks). Remission of depression was defined as a score of < 10 on the Montgomery-Asberg Depression Rating Scale and a score of < or = 2 on the Clinical Global Impressions scale at endpoint. Data were collected from November 2000 to February 2002. RESULTS: Twelve women (92.3%) concluded the 8-week adjunctive treatment; 11 subjects (91.6%) achieved full remission of depression. Symptoms that had persisted after an initial 4-week treatment with E(2) alone (e.g., tension, anxiousness, tiredness, and difficulty in concentrating) improved significantly (p <.05). Fifteen subjects concluded the treatment with citalopram monotherapy; 13 subjects (86.6%) showed full remission of depression. Anxiety and other somatic complaints had significant improvement (p <.05), while there was a trend toward improvement in vasomotor symptoms in those receiving monotherapy (p =.06). CONCLUSION: Citalopram alone is an efficacious treatment for perimenopausal and postmenopausal women with depression. Citalopram also appears to be efficacious as an adjunctive treatment for depressed subjects who remain symptomatic after treatment with E(2) (i.e., E(2) nonremitters). The role of citalopram monotherapy for the management of vasomotor symptoms warrants further investigation.

Effect of reproductive hormones and selective estrogen receptor modulators on mood during menopause.

Periods of intense hormonal fluctuations have been associated with heightened prevalence and exacerbation of underlying psychiatric illness, particularly the occurrence of premenstrual dysphoria, puerperal depression and depressive symptoms during perimenopause. It has been speculated that sex steroids such as estrogens, progestogens, testosterone and dehydroepiandrosterone (DHEA) exert a significant modulation of brain functioning, possibly through interactions with various neurotransmitter systems. It is therefore intuitive that abrupt alterations of these hormones would interfere with mood and behaviour. On the other hand, accumulating data suggest that hormonal interventions may also promote relief or even remission of depressive symptoms, as already demonstrated in studies with patients experiencing postpartum depression and perimenopausal depressive disorders. The extent to which perimenopause, alone, may increase the risk for depression is unclear. However, existing data strongly suggest that some women are particularly vulnerable to developing significant physical and psychological disturbances when entering perimenopause. This article reviews the effect of sex hormones and selective estrogen receptor modulators (SERMs) on mood among peri- and postmenopausal women. There are preliminary, though promising, data on the use of estradiol (particularly transdermal estradiol) to alleviate depression during perimenopause, use of a combination of estrogens and selective serotonin reuptake inhibitors for depression during the postmenopausal period, and the use of testosterone to improve psychological well-being and increase libido among women with induced menopause. Further studies would help to better delineate the usage of hormones as an antidepressant strategy (monotherapy or augmenting treatment) for peri- and postmenopausal women. A brief review of some nonhormonal interventions for the treatment of menopause-related symptoms that may significantly affect a woman's quality of life is also presented. There are some preliminary data suggesting the efficacy of antidepressants for the treatment of hot flushes; existing data on diet supplements and herbal products have shown more mixed results.

Ocorrência e tratamento de quadros depressivos por hormônios sexuais / Occurrence and treatment of depression by sex hormones

O processo de envelhecimento promove alterações significativas na produçäo e no equilíbrio dos níveis circulantes de diversos hormônios sexuais em homens e mulheres. Acredita-se que esses hormônios (estrógenos, progestógenos, testosterona, dehidroepiandrosterona [DHEA]) exercem papel modulador sobre diversas funções psíquicas, particularmente sobre o humor e a cogniçäo. Alterações nesse papel modulador causadas por variações abruptas dos hormônios sexuais circulantes -- como as que ocorrem, por exemplo, durante a transiçäo menopausal -- favorecem o surgimento de queixas depressivas. No entanto, a utilizaçäo terapêutica de hormônios sexuais pode promover alívio ou mesmo remissäo de sintomas depressivos, como já foi caracterizado com o uso de estradiol em mulheres em perimenopausa e com a administraçäo de testosterona após a menopausa. Este artigo aborda, por revisäo da literatura, os diversos papéis atribuídos aos hormônios sexuais no desenvolvimento e tratamento das queixas depressivas. Estudos sobre a eficácia terapêutica de estrógenos, testosterona e DHEA nos quadros depressivos säo discutidos de forma crítica. Em essência, existem resultados preliminares bastante promissores, particularmente quanto ao uso de estradiol e testosterona em subpopulações específicas para alívio de sintomas depressivos. Futuras investigações devem melhor definir a utilizaçäo de hormônios como agente depressivo monoterápico ou adjuntivo, bem como delinear os riscos e as contra-indicações associados a seu uso

Hormone treatment for mood disorders in women.

Periods of intense hormonal fluctuations have been associated with heightened prevalence and exacerbation of underlying psychiatric illness, particularly the occurrence of premenstrual dysphoria, puerperal depression and depressive symptoms during the menopausal transition. It has been speculated that sex steroids, such as estrogens, progestogens, testosterone and dehydroepiandrosterone, exert a significant modulation of brain functioning, possibly through interactions with various neurotransmitter systems. It is therefore intuitive that abrupt alterations of these hormones would interfere with mood and behavior. On the other hand, accumulating data suggest that hormonal interventions may also promote relief or even remission of depressive symptoms, as already demonstrated in studies on perimenopausal women treated with transdermal estradiol. This article reviews the potential role of sex hormones for the treatment of depressive disorders in women. There are preliminary, but promising data on the use of estradiol and testosterone for specific subpopulations. Further studies would help to better delineate the usage of these compounds as an antidepressant strategy (monotherapy or augmenting treatment).