Scientists highlight the contributions of Brazilian-made technique to cancer research and human genomics

The second day of the Genome Workshop 20+2 featured speakers who participated in the Human Cancer Genome Project and paid tribute to former FAPESP President Ricardo Brentani.

By Karina Toledo  |  Agência FAPESP – The groundbreaking idea of linking up scientists in different parts of São Paulo state via a virtual collaborative research network may have been key to the success of the FAPESP Genome Project, which began effectively in 1998 by setting out to sequence the genome of the bacterium Xylella fastidiosa. “What we did was create a virtual genomics institute. We were virtual when virtual wasn’t cool. We were virtual 20 years ahead of our time. And it was a brilliant move,” said British bioscientist Andrew Simpson, who ran the project.

Simpson was a keynote speaker on the second day (November 22) of the Genome Workshop 20+2. Part of the commemorations of FAPESP’s sixtieth anniversary, the workshop was held to celebrate the scientific leap that 22 years ago inaugurated research in genomics and molecular biology in Brazil.

“At the time, genomics was the thing. Everybody wanted to sequence something. But everybody except São Paulo made the mistake of trying to create a genomics institute. That takes time and money, and usually involves political squabbles. By the time we’d finished our genome, everyone else was still trying to build their institutes,” said Simpson, noting that the project achieved its goal six months ahead of schedule and under budget.

The success of the first stage enabled the virtual institute, known as ONSA (Organization for Nucleotide Sequencing and Analysis), to set itself even more audacious goals. The Human Cancer Genome Project (HCGP), its most ambitious venture, was launched in April 1999 to sequence genes expressed in some of the most common tumors in Brazil, using a novel methodology developed here. The HCGP was conducted by 29 laboratories and a bioinformatics center, with US$20 million in funding supplied by FAPESP and the Ludwig Institute for Cancer Research.

Necessity, the mother of invention

Known as ORESTES (short for “Open Reading frame Expressed Sequence Tags”), the sequencing technique used for the HCGP was developed during the PhD research of Emmanuel Dias Neto at the Federal University of Minas Gerais (UFMG), under Simpson’s supervision. Lacking the funds to investigate the genome of Schistosoma mansoni (the parasite that causes intestinal schistosomiasis) by conventional methods, the group created an alternative strategy based on PCR (polymerase chain reaction), a method that amplifies DNA and can be used to detect and measure specific genes.

Dias Neto described the technique in Proceedings of the National Academy of Sciences (PNAS) in 1997. At the time, he was invited by Ricardo Brentani, then President of FAPESP, to move to São Paulo, where he started a postdoctoral project at Hospital A C Camargo, now AC Camargo Cancer Center, focusing on the use of ORESTES to study cancer.

“In 1999, we submitted an application for funding for the HCGP. At the launch event, Fernando Reinach, one of the creators of the FAPESP Genome Project, said, ‘I’m very proud because in the Xylella project we studied a small organism for which we had no competitors and used the most traditional technology. Two years on, we’re challenging the established standard for human genome sequencing. Using technology developed in Brazil, we’re moving into the most competitive field and working on a really big genome’,” Dias Neto recalled in his presentation to the workshop.

The methods that were considered gold standards at that time focused on gene extremities, whereas the Brazilian method sequenced the central portion where the key genetic information is located. As the project advanced, it became evident that ORESTES could also be used to identify genes that are not among the most abundant in human tissue and were often overlooked in studies performed with traditional techniques. The group produced a large number of novel sequences, contributing to the international effort to decipher the human genome, which began in 1990 and reached completion in 2003.

“We had to be inventive because we weren’t able to do what everyone else was doing, but what we were doing was better,” Simpson said. “I’ve come to the conclusion that not only was it very good work, but it was highly underrated. Our contribution to the sequencing of the human genome was never really acknowledged.”

More than 1 million expressed sequence tags (ESTs) from different human tissues were sequenced via ONSA. Much of the data is available from the GenBank, a repository maintained by the US National Center for Biotechnology Information (NCBI). Even today the information produced by the group is used in research projects in this field.

“I remember Andy [Simpson] saying to me once, ‘You can spend the rest of your life working very hard on something that isn’t important. But if you devote your time and enthusiasm to something relevant, you’ll eventually do something good’,” Dias Neto said. “We have to do big science. We have to believe in ourselves.”

The second day of the Genome Workshop 20+2 also featured a talk by Sergio Verjovsky, who headed one of the ONSA laboratories and is now a researcher at Butantan Institute. He described his research on non-coding genes, once labeled “junk DNA” and considered unimportant. Scientists have now realized non-coding genes play a significant role as cellular regulators even though they do not encode proteins.

Another speaker was Rui Manuel Vieira Reis, Scientific Director of the Molecular Diagnosis Laboratory at Hospital de Amor (formerly the Barretos Cancer Hospital). The tumor bank maintained by the institution was set up in accordance with advice from Brentani, he recalled. Because patients treated at the hospital come from all over Brazil, these tumor specimens are highly diverse in genetic terms and are intensely used in cancer genomics research.

The session was chaired by Anamaria Aranha Camargo, who was on the HCGP team and is now Head Scientist at the Syrian-Lebanese Hospital in São Paulo. She is a member of FAPESP’s Adjunct Panel on Life Sciences.

Homage to Brentani

The last panel of the workshop paid tribute to Professor Ricardo Brentani, who died in 2011 and was considered one of the world’s leading cancer researchers. The panelists included Chi Van Dang, Scientific Director of the Ludwig Institute for Cancer Research. He presented an overview of the evolution of cancer genomics and outlined its contribution to patient care.

“We want to use genomics to intercept the development of cancer. I’m currently helping to lead an effort to create a pre-cancer atlas for breast and ovarian tumors relating to mutations in the gene BRCA. The goal is to look for clues to the earliest lesions in these tissues using single-cell sequencing techniques such as transcriptomics, proteomics and single-cell imaging. We hope that by using genomics we can learn from all this data and intercept the cancer by pharmacological or immunological means,” Dang said.

Other promising areas mentioned by Dang were liquid biopsy (analyzing tiny blood samples for tumor DNA) and metagenomics, which studies the influence of the microbiome on tumor development and response to treatment.

“Looking forward, I think the cancer microbiome is a great opportunity, where we – Ludwig and FAPESP – can play a role in future,” he concluded.

The other speakers who took part in the last panel were Marco Antonio Zago, President of FAPESP; Carlos Américo Pacheco, CEO of FAPESP; Paulo Hoff, Director of the São Paulo State Cancer Institute (ICESP); and Giovanni Guido Cerri, a professor at the University of São Paulo’s Medical School (FM-USP) and a former state health secretary.

“Brentani will always be remembered, as he’s one of the few people who managed to be at once a successful scientist, a science policymaker and the head of São Paulo’s largest cancer hospital at the time,” Zago said. 

Moreover, Brentani led the São Paulo branch of the Ludwig Institute for Cancer Research from its establishment in 1986 until his death in 2011.

“His most lasting legacy may derive from this job as head of the LICR, which led to the joining of Ludwig and FAPESP in one of the most impactful programs in FAPESP’s 60 years. The Genome Project, as it became known, transformed the science landscape in Brazil,” Zago said. “Brazilian biotech has matured to the point where its scientists are now players on the world stage. The competencies and expertise we began to acquire back then are highly valuable now. The legacy of this period extends to all fields of research in the life sciences.”

You can watch the full presentations of the event’s second day in the video below.