A new bioinformatic framework developed by researchers at University of California San Diego School of Medicine has identified key proteins significantly altered at the gene-expression level in biopsied tissue from patients with diabetic kidney disease, a result that may reveal new therapeutic targets.

In a recently published paper, researchers, led by Kumar Sharma, MD, professor of medicine at UC San Diego School of Medicine, revealed that the protein MDM2 was consistently down-regulated and played a key role in diabetic kidney disease progression. The researchers used the new “MetBridge Generator” bioinformatics framework to identify the relevant enzymes and bridge proteins that link human metabolomics data to the pathophysiology of diabetic kidney disease at a molecular level.

“MetBridge Generator allows for efficient, focused analysis of urine metabolomics data from patients with diabetic kidney disease, providing researchers an opportunity to develop new hypotheses based on the possible cellular or physiological role of key proteins,” said Sharma, senior author and director of the Institute for Metabolomic Medicine and the Center for Renal Translational Medicine at UC San Diego School of Medicine. “The framework may also be used in the interpretation of other metabolomic signatures from a variety of diseases. For example, MDM2 is also involved in regulating tumour protein p53, which is a target for cancer treatments.”

In a previous study, the authors identified 13 metabolites that were found to be altered in patients with diabetic kidney disease. Combining this information and publicly available data on metabolic pathways, the researchers tested an hypothesis that some proteins act as bridges creating less well-defined pathways. The framework then created a map of metabolic and protein-protein interaction (PPI) networks. This allowed the team to look deeper into relevant bridges with the greatest number of interactions with enzymes that regulate the 13-metabolite signature of diabetic kidney disease.

The authors already identified protein-RNA interactions as possible sources for additional key pathways underlying disease progression that could be added to the MetBridge Generator network. This growth will continue to add to possible therapeutic targets for disease treatment.

University of California – San Diego ucsdnews.ucsd.edu/pressrelease/new_bioinformatic_analysis_reveals_role_of_proteins_in_diabetic_kidney_dise

Researchers have identified a new pathway and with it a protein, BRD4, necessary for breast cancer cells to spread.

The findings may provide a new target to suppress breast cancer metastasis.

Triple-negative breast cancer is considered the worst subgroup of breast cancer. It is highly aggressive and responds poorly to the current therapeutic tools resulting in a dismal prognosis for patients. Furthermore, the lack of identified targets has limited the development of new drug strategies.

Researchers from Boston University School of Medicine (BUSM) used breast cancer cell lines that present the clinical characteristics of an aggressive breast cancer subtype (clinically described as a triple-negative breast cancer). They then used an experimental design to model cancer cell metastasis. By suppressing the expression of the protein BRD4 in these cell lines, they observed that their dissemination capabilities were blocked, indicating that BRD4 drives breast cancer dissemination. In addition, they conducted a screening analysis of human breast tumours and found that tumours with a high expression of BRD4 were more likely to metastasize.

“The current treatment options for a triple-negative cancer are unacceptably limited. It is crucial to identify new therapeutic targets to tackle challenging cancer types, including triple negative breast cancer. BDR4 targeting represents an innovative strategy to ablate breast cancer metastasis,” explained lead investigator Guillaume Andrieu, PhD, a post-doctoral research associate at Boston University School of Medicine.

Although obesity per se is not thought of as a carcinogen, the abnormal, inflamed microenvironments found in obesity are critical for progression, invasion and metastasis of triple negative breast cancer. “Bromodomain and ExtraTerminal domain (BET) proteins, which include BRD2, BRD3 and BRD4, are known to regulate production of inflammatory mediators. Our study proposes that BRD4 couples inflammation to breast cancer dissemination. Thus, small molecules that block BET proteins possess anti-inflammatory properties that can be useful for therapy,” he added.

Although these findings primarily focus on breast cancer and metastasis, the researchers plan to expand their results to the treatment of prostate cancer, which they believe has similar pathways involved in its metastasis.

Boston University Medial Center www.bu.edu/news/2016/11/15/researchers-identify-protein-required-for-breast-cancer-metastasis/

Autism is an agonizing puzzle, a complex mixture of genetic and environmental factors. One piece of this puzzle that has emerged in recent years is a biochemical cascade called the mTOR pathway that regulates growth in the developing brain. A mutation in one of the genes that controls this pathway, PTEN (also known as phosphatase and tensin homolog), can cause a particular form of autism called macrocephaly/autism syndrome.

Using an animal model of this syndrome, scientists from the Florida campus of The Scripps Research Institute (TSRI) have discovered that mutations in PTEN affect the assembly of connections between two brain areas important for the processing of social cues: the prefrontal cortex, an area of the brain associated with complex cognitive processes such as moderating social behavior, and the amygdala, which plays a role in emotional processing.

 “When PTEN is mutated, we find that neurons that project from the prefrontal cortex to the amygdala are overgrown and make more synapses,” said TSRI Associate Professor Damon Page. “In this case, more synapses are not necessary a good thing because this contributes to abnormal activity in the amygdala and deficits in social behavior.”

The study also showed that targeting the activity of the mTOR pathway shortly after birth, a time when neurons are forming connections between these brain areas, can block the emergence of abnormal amygdala activity and social behavioral deficits. Likewise, reducing activity neurons that project between these areas in adulthood can also reverse these symptoms.

‘Given that the functional connectivity between the prefrontal cortex and amygdala is largely conserved between mice and humans,” said TSRI Graduate Student Wen-Chin Huang, the first author of the study, “we anticipate the therapeutic strategies suggested here may be relevant for individuals on the autism spectrum.”

Although caution is warranted in extrapolating findings from animal models to humans, these findings have implications for individualized approaches to treating autism. “Even within individuals exposed to the same risk factor, different strategies may be appropriate to treat the symptoms of autism in early development versus maturity,” said Page.

The Scripps Research Institute www.scripps.edu/news/press/2016/20161115page.html

Many of the genetic variations that increase risk for schizophrenia are rare, making it difficult to study their role in the disease. To overcome this, the Psychiatric Genomics Consortium, an international team led by Jonathan Sebat, PhD, at University of California San Diego School of Medicine, analysed the genomes of more than 41,000 people in the largest genome-wide study of its kind to date. Their study reveals several regions of the genome where mutations increase schizophrenia risk between four- and 60-fold.

These mutations, known as copy number variants, are deletions or duplications of the DNA sequence. A copy number variant may affect dozens of genes, or it can disrupt or duplicate a single gene. This type of variation can cause significant alterations to the genome and lead to psychiatric disorders, said Sebat, who is a professor and chief of the Beyster Center for Genomics of Neuropsychiatric Diseases at UC San Diego School of Medicine. Sebat and other researchers previously discovered that relatively large copy number variants occur more frequently in schizophrenia than in the general population.

In this latest study, Sebat teamed up with more than 260 researchers from around the world, part of the Psychiatric Genomics Consortium, to analyse the genomes of 21,094 people with schizophrenia and 20,227 people without schizophrenia. They found eight locations in the genome with copy number variants associated with schizophrenia risk. Only a small fraction of cases (1.4 percent) carried these variants. The researchers also found that these copy number variants occurred more frequently in genes involved in the function of synapses, the connections between brain cells that transmit chemical messages.
With its large sample size, this study had the power to find copy number variants with large effects that occur in more than 0.1 percent of schizophrenia cases. However, the researchers said they are still missing many variants. More analyses will be needed to detect risk variants with smaller effects, or ultra-rare variants.

“This study represents a milestone that demonstrates what large collaborations in psychiatric genetics can accomplish,” Sebat said. “We’re confident that applying this same approach to a lot of new data will help us discover additional genomic variations and identify specific genes that play a role in schizophrenia and other psychiatric conditions.”

University of California San Diego Health health.ucsd.edu/news/releases/Pages/2016-11-22-study-finds-rare-genetic-variations-linked-to-schizophrenia.aspx

Most melanomas are driven by mutations that spur out-of-control cell replication, while nevi (moles composed of non-cancerous cells at the skin surface) harbouring the same mutations do not grow wildly. However, changes in the level of gene expression can cause nevi to become melanomas.

Dermatologists surmise that 30 to 40 percent of melanomas (approximately 30,000 cases per year) may arise in association with a nevus. However, clinicians would like to be able to better distinguish between the two, especially in borderline cases when they examine skin tissue after a patient biopsy.

Senior author John T. Seykora, MD, PhD, a professor of Dermatology in the Perelman School of Medicine at the University of Pennsylvania, led a study that found that decreased levels of the gene p15 represents a way to determine if a nevus is transitioning to a melanoma. The protein p15 functions to inhibit nevus cell proliferation.

“We showed that p15 expression is a robust biomarker for distinguishing nevus from melanoma,” said Seykora. “Making this distinction has been a long-standing issue for dermatologists. We hope that this new finding will help doctors determine if a nevus has transformed to melanoma. This could help doctors and patients in difficult cases. Current research will hopefully move this into the realm of standard practice in about one to two years.”

Decreased expression in the related protein p16 has also been associated with melanoma, but p15 appears to be a primary driver of oncogene-induced cell senescence in nevus cells. When p15 levels drop, then nevus cells begin to grow.

The team stained human nevus and melanoma tissue samples with p15 and p16 antibodies.  Staining was evaluated and graded for percentage and intensity to determine an “H score,” which correlates with the level of protein in the cells. This approach could also form the basis of a clinical determination, taking the form of an antibody test for p15 from a patient’s biopsy specimen. “If the staining level is high then that would be most consistent with a benign nevus,” Seykora said. “If the staining level is low then that would be consistent with a melanoma.”

RNA was also extracted from 14 nevus and melanoma tissue samples to determine levels of p15 mRNA.  The expression of p15 mRNA was significantly increased in melanocytic nevi compared with melanomas as determined by real-time quantitative RT-PCR analysis.

Penn Medicine www.uphs.upenn.edu/news/News_Releases/2016/11/seykora/