Friday, 7 December 2012

What's new from the annual conference of Italian Society of Human Genetics

The annual meeting of the Italian Society of Human Genetics (SIGU) has concluded a couple of weeks ago in Sorrento, a small beautiful town in southern Italy.
As usual, the meeting had a really busy schedule with several parallel sessions, so my report is not a complete survey but it's based only on talks I've attended.

The opening session was really inspiring, particularly the speech given by Prof. A. Ballabio from TIGEM on lysosomal function/biogenesis and autophagy. He presented his brilliant work on the genetic network controlled by TFEB transcription factor which tune the entire lysosomal compartment (published about 3 years ago on Science) and the recent findings on autophagy and how TFEB can also control this process. Besides the remarkable results themselves, I found this story interesting for how all the study has started. The starting point was one of the main concepts emerged from Systems Biology studies. It seems that every one of the main cell metabolic pathways is under the control of one or few master genes driving the co-expression of all the macinery needed for that specific function. Ballabio and his collaborators decided to screen the available gene expression databases (such as GEO) to find genes that are co-regulated in various conditions affecting the lysosomal compartment. They isolated a list of lysosomal related genes and analyzed in silico their promoter sequences to find shared transcription factor binding sites and finally tested which transcription factor binds to them. This led to the identification of TFEB as the master gene controlling lysosomal compartment. This demonstrates once more how an intelligent use of publicly available data generated from high-throughput studies could lead to new discoveries when the correct question is posed (and of course brilliant minds are at work on it...). Moreover Ballabio showed how the expression of TFEB is able to rescue the healthy phenotype in cells and mouse models affected by lysosomal storage disorders. This process is based on an augmented exocitosis of mature lysosomes, so that even if the catabolic enzymes remains nonfunctional, junk material no longer accumulates in the cells, strongly reducing its citotoxicity. Even if he admitted that the question remains on how to control the side effects and how to predict the long-term effects of the materials secreted by the cells, this strategy represents a promising opportunity for future therapies of lysosomal disorders.

At the conference there was a lot talking about clinical genetics and, interestingly, also clinical and diagnostic genomics. Genetic diagnosis based on NGS technology is attracting increasing attention, and this trend was clearly reflected in an increasing number of talks covering diagnostic use of NGS, even if doubts remain in the clinicians about its real accuracy and confidence.
In this area the two sponsored sections of both Life Tech and Illumina had interesting data to show. Indeed, under the pressure of the producers, the speakers also reported technical details on the protocols and performance, aspects that usually not receive a lot of attention. Benchtop sequenchers from both sides (essentially Life's Ion PGM and Illumina's MiSeq) have demonstrated that they are almost ready for a diagnostic and clinical debut, both with its own fallbacks that have been deeply discussed in the last months (see for example 1, 2, 3). Speaking for myself, I see a ready-to-go future for both platforms in the field of target re-sequencing of already known mutations or disease genes, with disease-targeted validated panels as the best option. This is in agreement to the trends emerged from Q&A sessions: small gene panels can guarantee higher coverage and so higher confidence in variant calling and moreover you get information only on the specific disease gene(s), avoiding more complex counseling and ethical issues. Even if exome sequencing proved to be an effective approach for syndromes showing extreme genetic heterogeneity or even better for rare conditions caused by private mutations, this approach still remain on the research side of the line. Technical difficulties related to data interpretation and accuracy, cost-benefit considerations and ethical issues raised by the genetic data not strictly related to the pathology have to be resolved before this approach could develop in a "routine" genetic test (however initiatives in this direction are already in testing, such as the Baylor College's Exome diagnostic service which has been running for a about one year and have already receive more than a hundred request for exome test from clinicians. See this interview on GenomeWeb).
Going back to presentations, it worth mentioning that Illumina made the move in clinical market, announcing that its MiSeq have received CLIA certification and so they are ready to sell a certified version of the machine (and the sequencing kits) from the second half of 2013. We'll see how Life Technologies will respond on its PGM to avoid the risk of being  cut out of the market...I think that IonTorrent's community based panels (target amplicon resequencing kits tailored on a specific pathology or cancer type and developed with the support and collaboration of research community) should allow them to rapidly develop robust disease oriented panels, but an official certification is still an essential requisite to compete in the clinical market.

An entire session was dedicated to non coding RNA. This kind of molecules were initially limited to rRNA and tRNA, but since their appearence on the regulatory scene with siRNA and miRNA, the catologue and relevance of ncRNA had rapidly increased. Today we have a lot of long non-coding RNA (lncRNA) and they have been implicated in basically every aspect of cell transcription regulation with a role also in pathological conditions (see fro example this review). Within the various talks, the one on facioscapularhumeral dystrophy (FSHD) has impressed me the most. The chromosomal locus associated with this pathology has been known from years. This locus contains a repetitive element of about 3kb and the pathological manifestations appears in subjects showing less than 10 (but at least 1) of these elements. In these subject the expression of a group of genes located in the region is altered and this lead to the observed phenotype. However the exact mechanism that connect the number of repeats with the modification in gene expression was not clear. In its presentation at SIGU, Gabellini from Milan showed its last results demonstrating that a lncRNA is involved in this process. This RNA is transcribed from the same genetic region linked to FSHD and it is partially encoded in the repeated element (so now it is explained why at least 1 repeat is needed to the pathology). This RNA acts in cis as an epigenetic factor: it binds to the repetitive elements and serve as binding site for a regulatory protein factor that repress the transcriptional activity of the entire locus (it seems that it can induce chromatin remodeling) . In affected subjects however, the reduced number of repeat elements also reduce the binding of the lncRNA and so the transcription level of genes in this region increase, leading to pathology.
In another talk Gustincich from Trieste showed how lncRNA could also act in stimulating translation. The fact itself confirm new possibilities for the regulatory role of non-coding RNA, since until now they have been mostly implicated in repression of transcription. This enrich the picture of protein level regulation that appear to occur at three distinct levels (plus post-traductional mechanisms of course): mRNA transcription, regulated by historically studied mechanisms such as TF binding and chromatin remodeling  which made the transcript available; RNA stability and traduction, regulated by availability of specific RNA-binding factors; and a fine regulation of mRNA levels and mRNA traduction based on ncRNA or more complex mechanism such as RNA editing. Things are made even more complicated by the fact that often a single ncRNA could target multiple mRNAs with different affinity and so its effect on protein level depends on the final equilibrium of all the possible interactions, as illustrated by the theory of competing endogenous RNA (ceRNA) appeared on Cell.

Making the rest of the story short, I've seen an increasing attention on CNV and their role in pathological conditions; there was also a session dedicated to new protocols in genetic therapy and interesting talks on mitochondria related pathology (this field has taken advantage of NGS technology too).

Walking around poster session I've noticed that almost all of the project presented involving exome sequencing were case studies on rare syndromes or even on unique patients showing a peculiar phenotype. The idea is relatively simple: you have and affected subject with an unusual phenotype or a clinical diagnosis but unknown molecular defect, luckily you have access also to genetic material from its relative and a family tree from which to assess the model of genetic transmission...Now you can perform exome sequencing on the affected subject and (at least) its parents and try to identify the causative mutation(s). This approach has demonstrated to be extremely effective and new papers applying this method have being published almost every day in the last year. Often, this is reported as diagnostic exome sequencing, since the final result is a molecular diagnosis for a yet unknown case. There is a double advantage in this process: first, the research group identify the genetic defect and can make assumption on the molecular mechanism underlying the pathology (and this may lead also to treatment); second, we got new knowledge on gene function and gene-to-phenotype relationships. This latter aspect is of major interest for medical research, since a better knowledge of genes function is one of the main missing factor preventing researcher to make prediction about the SNVs identified by NGS studies. Now that the new technologies have made sequencing on sporadic and ultra-rare cases affordable, research groups could also reanalyze old families remained undiagnosed and our knowledge of gene function will rapidly increase.

Ok, I've wrote enough...even if a lot more should be written indeed!
Keep your genetic enthusiasm alive!

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