Category Archives: Genetic medicine

Edet E Udo, Samar S Boswihi, Bindu Mathew, Bobby Noronha, Tina Verghese, Aisha Al-Jemaz, Fatma Al Saqer

Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, Kuwait

Correspondence: Edet E UdoDepartment of Microbiology, Faculty of Medicine, Kuwait University, P. O. Box 24923, Safat 13110, KuwaitTel +965 498 36773Fax +965 2533 2719Email edet@hsc.edu.kw

Purpose: Methicillin-resistant S. aureus (MRSA) belonging to clonal complex 15 (CC15-MRSA) is rare among clinical isolates with few reports from retail camel meat and human patients. This study investigated the genetic relatedness of CC15-MRSA isolated for the first time from patients in Kuwait hospitals.Methods: Antibiotic susceptibility was tested by the disk diffusion method. Minimum inhibitory concentration was determined using Etest strips. Molecular typing was performed using spa tying, multilocus sequence tying and DNA microarray.Results: Of 1327 MRSA isolates, 42 (3.1%) were identified as CC15-MRSA. The 42 isolates belonged to sequence type ST1535-harbored SCCmec type V and spa types t084 (36 isolates), t346 (3 isolates) and one of t114, t228 and t7583. All 42 isolates were resistant to gentamicin, kanamycin, fusidic acid and cadmium acetate; 38 isolates were resistant to tetracycline. The isolates harbored aacA-aphD and fusC that codes for gentamicin and fusidic acid resistance, respectively. Tet(K) was present in the tetracycline-resistant isolates. In addition, the 42 isolates carried inu(A) (lincosamide nucleotidyltransferase) that confers resistance to lincomycin and clindamycin although phenotypically susceptible to these antibiotics. The isolates belonged to accessory gene regulator type II and capsular polysaccharide group 8 but lacked genes for Staphylococcus enterotoxins, toxic shock syndrome toxin, collagen-binding adhesins and PantonValentine leukocidin.Conclusion: This study revealed the emergence and transmission of a previously rare MRSA clone among human patients in Kuwait hospitals and highlights the increasing infiltration of rare MRSA into the human population.

Keywords: DNA microarray, MRSA, antibiotic resistance, MLST

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CHAMPAIGN, Ill. With a new CRISPR gene-editing methodology, scientists from the University of Illinois at Urbana-Champaign inactivated one of the genes responsible for an inherited form of amyotrophic lateral sclerosis a debilitating and fatal neurological disease for which there is no cure. The novel treatment slowed disease progression, improved muscle function and extended lifespan in mice with an aggressive form of ALS.

ALS unfortunately has few treatment options. This is an important first step in showing that this new form of gene editing could be used to potentially treat the disease, said bioengineering professor Thomas Gaj, who co-led the study with bioengineering professor Pablo Perez-Pinera.

The method relied on an emerging gene-editing technology known as CRISPR base editors.

Traditional CRISPR gene-editing technologies cut both strands of a DNA molecule, which can introduce a variety of errors in the DNA sequence, limiting its efficiency and potentially leading to a number of unintended mutations in the genome. The Illinois group instead used base editing to change one letter of the DNA sequence to another without cutting through both DNA strands, Perez-Pinera said.

Base editors are too large to be delivered into cells with one of the most promising and successful gene therapy vectors, known as adeno-associated virus, Gaj said. However, in 2019, Perez-Pineras group developed a method of splitting the base editor proteins into halves that can be delivered by two separate AAV particles. Once inside the cell, the halves reassemble into the full-length base editor protein.

By combining the power of AAV gene delivery and split-base editors, Gaj and Perez-Pinera targeted and permanently disabled a mutant SOD1 gene, which is responsible for roughly 20% of inherited forms of ALS. They published their results in the journal Molecular Therapy.

Many ALS studies are focused on preventing or delaying the onset of the disease. However, in the real world, most patients are not diagnosed until symptoms are advanced, said graduate student Colin Lim. Slowing progression, rather than preventing it, may have a greater impact on patients. Lim is the co-first author of the study along with graduate students Michael Gapinske and Alexandra Brooks.

CRISPR base editing decreased the amount of a mutant protein (blue) that contributes to ALS in the spinal cord. Left, a spinal cord section from an untreated mouse. Right, a spinal cord section from an animal treated by base editing.

Image courtesy of Thomas Gaj

Edit embedded media in the Files Tab and re-insert as needed.

The researchers first tested the SOD1 base editor in human cells to verify reassembly of the split CRISPR base editor and inactivation of the SOD1 gene. Then they injected AAV particles encoding the base editors into the spinal columns of mice carrying a mutant SOD1 gene that causes a particularly severe form of ALS that paralyzes the mice within a few months after birth.

The disease progressed more slowly in treated mice, which had improved motor function, greater muscle strength and less weight loss. The researchers observed an 85% increase in time between the onset of the late stage of the disease and the end stage, as well as increased overall survival.

We were excited to find that many of the improvements happened well after the onset of the disease. This told us that we were slowing the progression of the disorder, Gapinske said.

The base editor introduces a stop signal near the start of the SOD1 gene, so it has the advantage of stopping the cell from making the malfunctioning protein no matter which genetic mutation a patient has. However, it potentially disrupts the healthy version of the gene, so the researchers are exploring ways to target the genes mutant copy.

Moving forward, we are thinking about how we can bring this and other gene-editing technologies to the clinic so that we can someday treat ALS in patients, Gaj said. For that, we have to develop new strategies capable of targeting all of the cells involved in the disease. We also have to further evaluate the efficiency and safety of this approach in other clinically relevant models.

The split base editor approach has potential for treating other diseases with a genetic basis as well, Perez-Pinera said. Though ALS was the first demonstration of the tool, his group has studies underway applying it to Duchenne muscular dystrophy and spinal muscular atrophy.

The Muscular Dystrophy Association, the Judith and Jean Pape Adams Foundation, the American Heart Association and the National Institutes of Health supported this work. Gaj and Perez-Pinera are affiliated with the Carl R. Woese Institute for Genomic Biology at Illinois. Perez-Pinera also is affiliated with the Carle Illinois College of Medicine and the Cancer Center at Illinois.

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Are you genetically predisposed to some diseases? Do you carry genetic mutations that can impact the health of your child? A debit card-sized IndiGenome card, recently unveiled by the government, will help you find the answers if your genetic information is captured in a database that India's umbrella research organisation - the Council of Scientific and Industrial Research (CSIR) - is building. Once your genome is sequenced from your blood sample and added to this database, the card can be used to read the information embedded in your genes, just as your debit card is used to generate a financial transaction statement from your bank's database.

Well, the card is not the key. Genome sequencing - or mapping the pattern of the basic building block of every living cell - is. A genome contains all of a living being's genetic material (simply put, the genome is divided into chromosomes, chromosomes contain genes, and genes are made of DNA). Each genome has approximately 3.2 billion DNA base pairs, and the way they are arranged, or variations and mutations in their pattern, can provide clues about the individual's health or ill health, inherited or acquired. Already, 1,008 individuals, chosen to represent India's social, ethnic and geographic diversity, have been issued such cards. Over 280 doctors in 70 institutions have been trained to make sense of such data. A CSIR institute, the Institute of Genomics and Integrative Biology (IGIB) - which is spearheading the Genomics for Public Health in India, also called IndiGen project - is planning to enrol 20,000 Indians for whole genome sequencing in the next couple of years to build a larger database. The data will be important for building the knowhow, baseline data and indigenous capacity in the emerging

area of precision medicine. IndiGen will have applications in a number of areas, including faster and more efficient diagnosis of rare diseases. The other benefits are cost-effective genetic tests, carrier screening applications for expectant couples, enabling efficient diagnosis of heritable cancers and pharmacogenetic tests to prevent adverse drug reactions.

In fact, IGIB leads two other programmes - Genomics for Understanding Rare Diseases India Alliance (GUaRDIAN) Network and Genomics and other Omics tools for Enabling Medical Decision (GOMED), led by Dr Mohammed Faruq, to see that the genome database and genetic screening leads to development of cost effective diagnostic tools and tests that are licensed out to private and public medical institutions.

The world over, fall in cost for genome sequencing (a reason for which is increase in computing power) is leading to path-breaking applications spanning the entire spectrum of healthcare - diagnosis to treatment and drug development to prevention and wellness - and unrelated fields such as agriculture, animal productivity, environment, sports and many more. Consider this: CSIR took six months to sequence the genomes of 1,008 Indians. Seventeen years ago, a global initiative led by the US National Academy of Sciences, had taken 12 years, and spent $3 billion, to complete the sequencing of the first human genome. Today, sequencing a person's genome does not cost more than $1,000. In fact, Sam Santosh, Chairman of MedGenome Labs, a private venture, says he can sequence a complete human genome in his Bengaluru lab for $500-600.

The Industry

The catalyst for the IndiGen project was advent of Next Generation Sequencing (NGS) in the last decade or so. (NGS helps an entire human genome to be sequenced in a day. The previous Sanger sequencing technology used to take over a decade.) The technology is being used by both IGIB and MedGenome for high-throughput sequencing, i.e. sequencing hundreds of thousands of genes in one go.

IndiGen is a good start but there are countries that are much ahead. Genomics England, a public-private partnership between the UK government and world's biggest NGS sequencing machine maker, Illumina, has completed sequencing of 1,00,000 genomes of British citizens comprising a mix of cancer patients, rare disorder patients and healthy people. A new agreement for sequencing of 3,00,000 genomes, with an option to increase it to 5,00,000 over the next five years, was signed by the two partners on January 13. "Countries such as Estonia and Iceland are attempting to sequence every single citizen and link the data with their health schemes. The US has decided to do it for every single rare disorder patient," says Praveen Gupta, Managing Director & Founder, Premas Life Sciences - the authorised partner of US-based Illumina in India.

"The global high-throughput genomics industry will be in the range of $10-12 billion. With an estimated 25-30 per cent annual growth, it is expected to become a $25-30 billion market in the next three-four years," he says. Premas sells tools (reagents, platforms, software, training) to labs that do genetic testing in India. With 90 per cent market share, it drives NGS technology in India, too. "The high-throughput genomics market in India, including reagents, instruments and services, will be about Rs 500 crore. Approximately 50,000 samples must be reaching India's clinical (service) market on an annual basis," says Gupta.

Dr Sridhar Sivasubbu and Dr Vinod Scaria, IGIB scientists at the forefront of the IndiGen programme, say genome sequencing is just one piece of the initiative. IGIB has two other programmes - Genomics for Understanding Rare Diseases India Alliance (GUaRDIAN) Network and Genomics and Other Omics Tools for Enabling Medical Decision (GOMED) - to ensure their genome database and genetic screening lead to development of cost-effective diagnostic tools and tests that can be licensed out to private and public healthcare institutions. "GUaRDIAN focuses on rare diseases. Given that we are a billion-plus people, even the rarest of the rare diseases is found in a few lakh people. So, this programme caters to 70 million people living with some genetic disease. We find technological solutions for these 7,000-odd diseases and partner with a network of 280 clinicians across 70-odd institutions to offer our solutions," says Sivasubbu.

"Patients and their families connect with us through the GUaRDIAN network. We sequence their genes to find the mutation, and once we find it, we go back to their communities with a cost-effective test to identify that mutation. You just have to look for that single mutation in others, and that's cost-effective," says Scaria. Instead of whole genome sequencing, which costs between Rs 50,000 and Rs 1,00,000, a single assay developed by IGIB through these programmes costs Rs 2,000. The team led by Sivasubbu and Scaria has developed 180 tests for 180 genes and transferred the technology to private diagnostic labs. The institute itself has catered to about 10,000 patients and carried about 25,000 tests in the last two years. "We have entered into partnerships with about a dozen companies. The format of the collaboration depends on the business models they follow," says Sivasubbu.

Premas Life Sciences

The authorised partner of US-based Illumina in India provides tools (reagents, platforms, software, training and troubleshooting) to labs engaged in genetic testing in India. With 90 per cent market share, it drives the New Generation Sequencing technology in India

It works in areas other than healthcare, too. For example, Tagtaste, an online platform for food professionals, uses the company's services to understand the genomics of taste. It has customers and partners such as Pepsico, Coca Cola, Nestle and ITC

Dr Lal PathLabs

The company has licensed diagnostic tests for 27 conditions from Institute of Genomics and Integrative Biology (IGIB)

Has a portfolio of more than 200 different types of tests

It is active in fields like rep- roductive health, cancer di- agnosis, pharmacogenomics

Medgenome Labs

The Bengaluru-based player considers itself as the private sector avatar of IGIB. It offers not just genetic tests but also carries out research. It has collaborated with Singapore's Nanyang Technological University to sequence 1,00,000 whole genomes from Asia. The Genome Asia project has already completed sequencing 10,000 whole genomes, of which about 8,000 are from India

MedGenomes research associates recently sequenced and analysed the genome of the Cobra snake. The findings, published in Nature, suggest the possibility of developing a new method of producing anti-venom completely in the lab.

Lifecell International

The company is in the genetic testing space. It has tied up with IGIB and offers tests ranging from basic screening (prenatal screening, newborn screening, etc) to high-end ones based on NGS. It tests more than 50,000 patient samples every month

Mahajan Imaging

The company has set up a new R&D wing to focus on cutting-edge scientific and clinical research and help radiology and genomics companies develop world-class clinically relevant products. The idea is to integrate imaging and genomic data

Trivitron Healthcare

The Chennai-based chain wants to develop tools using genomic data that can work on conventional platforms. It is talking to IGIB and trying to get its knowhow for manufacture of products for sale to pathology labs

The Private Hand

Dr Lal PathLabs, a pathology lab chain with big plans in the genetic testing space, has an entire department for such tests. "We offer tests of all levels - Karyotyping, which looks at the macro level, Microarrays, which offer intermediate resolution, and NGS, used to elucidate the DNA sequence at the micro level. The fields we are active in include prenatal reproductive health, cancer diagnosis and pharmacogenomics (study of how genes affect a person's response to drugs). We have more than 200 tests and conduct around 300 tests per day," says Dr Vandana Lal, Executive Director, Dr Lal PathLabs. The company has licensed tests for 27 conditions from IGIB. "The imported technology is expensive. The idea to partner with CSIR labs is to bring these cutting-edge technologies to Indian masses at a reasonable cost," says Dr Lal.

Lifecell International is another player in the genetic testing space that has tied up IGIB. "We offer tests ranging from basic screening (prenatal screening, newborn screening, etc.) to high-end ones based on NGS. We test more than 50,000 samples a month. PCR-based tests range from Rs 2,000-5,000 whereas tests based on NGS and those involving sequencing of large parts of the genome can cost upwards of Rs 20,000," says Ishaan Khanna, CEO, Biobank & Diagnostics, Lifecell. He believes the IndiGen database will help in development of better analysis and interpretation tools. "Our focus is on developing rapid genome testing for children in NICU (Neonatal ICU) and similar other scenarios where doctors need clear actionable results in the shortest possible time. IndiGen provides the right mix of Indian genome database," he says.

But not every partnership is for access to cost-effective tests. Mahajan Imaging, a medical imaging chain, has set up a Centre for Advanced Research in Imaging, Neuroscience and Genomics to focus on research and helping radiology and genomics companies develop clinically relevant products. The idea is to integrate imaging and genomic data. "We started the project six months ago and are among the first imaging companies to get into genomics. In the next three-five years, it will be possible for an AI algorithm to look at the radiology image and give genomic readings on it," says Vidur Mahajan, Associate Director, Mahajan Imaging.

Chennai-based Trivitron Healthcare sees in IndiGene data an opportunity to develop multiple testing platforms. It wants to develop tools using genomic data that can work on conventional platforms. "There are almost 1,00,000 pathology labs in India. Hardly 500-1,000 must be doing genetic testing. Companies like ours are talking to IGIB and trying to get the knowhow to manufacture products for a larger population," says Jameel Ahmad Khan, Head, R&D, Trivitron. "IGIB will develop the knowhow, provide proof of concept, and we will convert it into a product which pathology labs without highly trained manpower can also run," he says.

Bengaluru-based Medgenome Labs considers itself a private sector avatar of IGIB, perhaps even a couple of years ahead in research and development. The company not only does genetic tests but also carries out research. It has collaborated with Singapore's Nanyang Technological University to sequence 1,00,000 whole genomes from Asia. The Genome Asia project has already completed sequencing of 10,000 whole genomes, of which about 8,000 are from India. On December 4, international journal Nature published the initial findings from the project - genetic variation, population structure, disease associations, etc., from a whole-genome sequencing reference dataset of 1,739 individuals of 219 population groups and 64 countries across Asia. "We sequence a person's genes and other relevant parts of the genome for specific mutations to understand what is causing the disease and specific drugs and dosage the person will respond to. We also help pharmaceutical companies understand genomes and discover new drug targets and biomarkers," says Sam Santosh, Chairman, MedGenome. With about 120 sales people, the company claims it is generating samples from around 10,000 clinicians across the country. "We were the first to enter the market. In that sense, we created the market, and would be having 60-65 per cent market share. The sequencing market must be in the range of $70-75 million," says Santosh. The company expects its diagnostic business to touch $100 million in four years. Interestingly, MedGenome's research associates recently sequenced and analysed the genome of Cobra snake. The findings, published in Nature, suggest the possibility of developing a new method of producing anti-venom completely in the lab.

Other Sectors

Illumina's India partner Premas Life Sciences is not selling its next generation sequencers only to healthcare firms. Gupta says it has more than 200 installations in India alone. "Anything which is living has a DNA nucleic acid and can be sequenced. We have a mass research market and practically every institute has the sequencer. Somebody will be working on cow, somebody on rice, a third institute on some bacteria," says Gupta.

IGIB researchers Dr Sridhar Sivasubbu and Dr Vinod Scaria vouch for this. The institute is getting requests, including partnership offers, from non-medical players. Tagtaste, an online platform for food professionals, wants to understand the genomics of taste. "In a lighter vein, you could say that the efficiency of a professional wine taster depends on his genes," says Scaria. With customers and partners such as Pepsico, Coca Cola, Nestle and ITC, and a clientele that includes chefs of global hotel chains, taste is serious business. "The point is, if a person is paying Rs 3,000 for a curry or Rs 5,000 for a soup, you better get the taste right," says Scaria. IGIB also works with Adam's Genetics for R&D and product development in the area of fitness. "One of the companies works in the cricket industry. Each player can be genetically tested for performance and food intake because not all muscles have the same size and some people gain weight, some don't gain muscle mass, while some may be more prone to injury. Genetic tests can find out who is prone to injury, or whether weightlifting is the right exercise for a player or not," says Sivasubbu.

The Future

Indians are 17 per cent of the world's population. But only 0.2 per cent genomic data is from the Indian population. This is one area where India can lead. We have so many diseases, and if we can provide the genetic design, the world can develop diagnostics and therapies. "We can create ideas. We didn't invent computers but we created the IT industry. In the same way, we didn't invent genomic sequences but tomorrow we can create a genome informatics economy," says Premas' Gupta.

There are other possibilities, too. "A lot of pundits say that in the next five-six years, 15 per cent of the world's population will be whole genome sequenced. If I require 100 GB data for a genome sequence, for 1.5 billion people, 25-30 exabytes of data will be needed. The entire data content on YouTube, globally, is 0.8 exabytes. Imagine the kind of data generation and analytics possibilities we are talking about," says Gupta. "We need people to analyse this data. If we can take the lead and train our manpower, we can move the world, we can create a new industry which can lead for the next 20 years just the way the IT industry did," he adds. Incidentally, Gupta claims that TCS has already bought Illumina's sequencing platform. So has WIPRO. It seems IT companies are already sensing an opportunity.

Sivasubbu says it took India 10 years to scale up from sequencing one genome to 1,000 genomes. "In the next decade, it may be a million."

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The Gene Business - Business Today

Atlantic Health System Cancer Care is dedicated to providing patients with access to the most promising and life-saving trials, research, and innovations in the communities where they live and work. Cutting-edge initiatives include the following:

In affiliation with the Translational Genomics Research Institute (TGen) of Phoenix, AZ, Atlantic Health System Cancer Care has created the nations firstBreakthrough Oncology Accelerator, a pioneering research and clinical collaboration that offers multiple early and late-phase clinical trials, right here in New Jersey. The Accelerator is designed to improve patient access to life-saving therapies through more rapid deployment of new research trials and novel payment mechanisms post-approval, saidEric Whitman, MD, medical director of Atlantic Health System Cancer Care.

The Breakthrough Treatment Center is part of the Breakthrough Oncology Accelerator and offers phase 1 clinical trials using the latest immunotherapies, cell-based therapies and genetic medicine options to cancer patients who have not responded to other treatments. The Center typically accommodates eight to 14 patients daily.

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We treat all patients with advanced cancers and use all kinds of treatment, saidDr. Angela Alistar, medical director of the Breakthrough Treatment Center who came to Morristown Medical Center from Wake Forest University a few years ago. She is widely known for her pioneeringresearch on pancreatic cancer, which has doubled the patient survival rate.

As a physician, I always look for early-phase studies because I know what standard of care can do. Unless I have a curative standard of care treatment, Im not interested. I want to do better. I want to find a clinical trial that combines standard of care with something exciting that has promise. Im always looking for, How can we do better? Thats what this Center is about: Not waiting until the last minute, but giving our patients the best options up front.

Atlantic Health System Cancer Care is also the lead affiliate ofAtlantic Health Cancer Consortium (AHCC), the only New Jersey-based Community Oncology Research Program (NCORP) designated by the National Cancer Institute (NCI). Covering 73% of the states population, the AHCC NCORP presents a substantial opportunity to advance scientific understanding of cancer prevention, screening, control, treatment and care delivery research within a large and diverse population, saidMissak Haigentz, MD, medical director of Hematology and Oncology for Atlantic Health System and principal investigator for AHCC NCORP.

To learn more about Atlantic Health System cancer research trials, please go toatlantichealth.org/research

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PARP inhibitors interfere with cancers ability to repair damage to its DNA. They are becoming increasingly useful in treating ovarian cancer.

Valencia Halls oncologist wanted to give her the best possible chance of staying in remission, so in June 2017, she prescribed Zejula (niraparib), a once-daily oral treatment thats part of an emerging class of medicines known as poly (ADP-ribose) polymerase (PARP) inhibitors. Just a few months before Valencia Halls disease returned, Zejula had become the first PARP inhibitor approved by the Food and Drug Administration (FDA) to treat women with recurrent ovarian cancer who do not have a genetic abnormality but previously responded well to platinum-based chemotherapy. Valencia Hall was a perfect candidate for the drug, which is referred to as a maintenance treatment because its prescribed with the goal of preventing ovarian cancer from returning.

She has been free of the disease since starting Zejula and has experienced no side effects, aside from a temporary drop in platelet counts that her oncologist corrected by dialing down Valencia Halls daily dose. Zejula has allowed me to live my life as I see fit, says Valencia Hall, 51, a freelance graphic artist in Phoenix. Its an oral medication, so I dont have to go in for infusions. The opportunity to have this as a maintenance therapy is exciting its hope.

Zejula is one of three PARP inhibitors that are taking an increasingly prominent role in ovarian cancer treatment and improving patients prognosis. With dozens of clinical trials underway, including some that seek to combine PARP inhibitors with other cancer treatments, that role could expand even more.

Drugs in this class work by inhibiting the PARP enzyme, which normally helps damaged DNA repair itself. Preventing this repair causes cancer cells to die, especially those that already have DNA repair defects due to a mutated BRCA 1 or 2 gene or other abnormalities. So far, clinical trials have shown that these drugs can lengthen the time until the disease progresses; their impact on the length of life is still being investigated. For women using a PARP inhibitor for maintenance, the drugs can help increase the time between courses of chemotherapy for recurrent disease.

In the past, we would take patients who had a high risk of recurrence and just watch them until cancer came back because we didnt have maintenance therapies that were effective, tolerable or convenient, says Dr. Bradley Monk, a professor and director of the division of gynecologic oncology at Creighton University School of Medicine at St. Josephs Hospital and Medical Center in Phoenix, Arizona, and also medical director of gynecologic oncology research for the U.S. Oncology Research Network. PARP inhibitors have been significant because theyre expanding the treatment opportunity for many patients, he adds.

Each year, more than 22,000 women in the U.S., about half of whom are over age 63, receive a diagnosis of ovarian cancer, according to the American Cancer Society. A small proportion of women have inherited mutations in BRCA1, BRCA2 or other cancer-related genes that raise their risk of ovarian cancer and can take steps to fend off the disease, including surgery to remove their ovaries. But most cases occur out of the blue, and because the symptoms can be vague and easily overlooked, like bloating or stomach pain, many women do not receive a diagnosis until the disease has advanced to the point where it can be hard to treat. The disease will recur in about 85% of women who initially respond to chemotherapy.

For women with ovarian cancer, PARP inhibitors have been an option since 2014, when the FDA approved Lynparza (olaparib) as a maintenance therapy for patients with BRCA mutations who had received three or more chemotherapy treatments. Rubraca (rucaparib) followed in 2016 and Zejula in 2017.

PARP INHIBITORS REACH MORE PATIENTS

Over the past two years, the FDA approved more uses of PARP inhibitors so that many more patients can benefit from these medicines and access the drugs earlier in treatment. In April 2018, Rubraca was approved as a maintenance therapy to treat recurrent ovarian cancer in women who responded at least partially to platinum-based chemotherapy, whether or not they had a genetic mutation. That December, Lynparza was approved as a first-line maintenance treatment for BRCA-mutated ovarian cancer, meaning patients can be given the drug after successfully completing just one round of platinum-based chemotherapy.

That was based on a clinical trial showing the drug reduced the rate of disease progression or death by 70%.

Most recently, in October 2019, the FDA approved Zejula for use in patients with advanced ovarian cancer associated with a cellular abnormality called homologous recombination deficiency. BRCA1 and BRCA2 are two of these types, but in ovarian cancer, about 17 other such genetic abnormalities can drive the disease. Between 41% and 50% of ovarian tumors are thought to have homologous recombination deficiency, which can be detected with a tumor test, Myriad myChoice CDx, that the FDA also approved last October.

In a clinical trial leading to the approval, 24% of participants with homologous recombination deficiency-positive ovarian cancer responded well to Zejula, experiencing some tumor shrinkage. That may not sound like a high response rate, but it surpasses the overall response rate to PARP inhibitors among all patients with ovarian cancer either with or without mutations, says lead clinical trial investigator Dr. Kathleen Moore, associate professor of gynecologic oncology at Stephenson Cancer Center at the University of Oklahoma.

These are heavily pretreated patients in which the response rate has typically been 12%, so this was double what we normally see, Moore says. The clinical benefit here was quite high. She adds that patients with BRCA mutations did particularly well: Nearly 40% of those who previously responded well to platinum-based chemotherapy responded to Zejula. The most common side effects include gastric upset, mouth sores, rash, headache and dizziness. The drug can also cause anemia and abnormal blood counts, which, in rare cases, can lead to myelodysplastic syndrome, a bone marrow problem, or the blood cancer acute myeloid leukemia.

As PARP inhibitors continue to help a widening population of patients with ovarian cancer, a push is underway to use them earlier in the treatment process. Several trials presented at the 2019 European Society for Medical Oncology conference demonstrated the potential value of that strategy.

One study found an 84% survival rate among patients who took Zejula for two years following chemotherapy, regardless of their homologous recombination deficiency status, compared with 77% who got a placebo. The median progression-free survival period (time from treatment to disease progression) for patients taking the drug was 14 months compared with eight months for those on placebo.

Another study evaluated an investigational PARP inhibitor, veliparib, combined with chemotherapy as a first-line treatment followed by veliparib alone for maintenance. Median progression-free survival among patients on that regimen was 23.5 months versus 17.3 months for those taking a placebo.

The third trial presented at the conference involved Avastin (bevacizumab), a drug that cuts off the blood supply to tumors. The FDA approved Avastin in 2018 to treat advanced ovarian cancer in conjunction with chemotherapy.

During the more recent trial, patients with newly diagnosed advanced ovarian cancer took Avastin plus chemotherapy, followed by Avastin with Lynparza for maintenance. Those who took Lynparza along with Avastin had a median progression-free survival of 22 months compared with 17 months for those who received Avastin and a placebo.

In all three studies, progression-free survival rates were the highest among homologous recombination deficiency-positive patients, but the fact that PARP inhibitors extended survival even among those without those mutations was encouraging to oncologists who treat ovarian cancer.

These were all positive studies that undoubtedly show that PARP inhibitor maintenance following chemotherapy will extend beyond BRCA-associated ovarian cancer, Moore says. Its highly likely that a much larger proportion of women with ovarian cancer who are diagnosed in 2020 will receive a PARP inhibitor (than in previous years). Women will be able to live longer with their cancer because were developing effective therapies that push out progression-free survival.

COMBINATIONS GAIN STEAM

A clinical trial investigating a novel PARP combination proved a lifesaver for Diane Sarver, who first received a diagnosis of ovarian cancer in 2010. Chemotherapy put her cancer in remission three times, but when she relapsed again in 2015, she decided to search for a novel treatment strategy and traveled from her home in Lake Oswego, Oregon, to The University of Texas MD Anderson Cancer Center in Houston.

Sarver was entered into an early-phase trial combining Lynparza with the investigational drug AZD2014, which interferes with a cellular pathway (called phosphatidylino-sitol-3 [PI3] kinase) that drives resistance to PARP inhibitors. Within seven weeks of starting the combination therapy which consists of two oral drugs taken twice a day , Sarvers ovarian cancer came under control. As part of the ongoing trial, she continues to take the two drugs, which, she says, have caused no side effects and shes still disease-free.

Whats notable about Sarvers case is that she didnt inherit any genetic mutations that would predict such a long-lasting response to PARP inhibitors. Although her tumor tested positive for a rare BRCA mutation, it was considered nonactionable scientists did not yet know whether or not the mutation produced an aberrant protein that would make it likely to respond to the drug combination being studied. The theory behind the trial is that blocking PI3 kinase may transform tumors that would not normally respond to PARP inhibition into responders.

Im amazed that Ive had such a good outcome, says Sarver, 69, a retired clinical technologist and mother of two grown children. Her only limitation is that she has to fast two hours before and after taking the drugs, she says, but the lack of side effects has given her the freedom to travel, speak to medical students about her experiences and spend time with her family.

Ive seen both children through their college graduations, Sarver says. I feel completely functional and am grateful to have never experienced any fatigue or other physical restriction.

MD Anderson is now planning several midstage clinical trials combining PARP and PI3 kinase inhibition, including one that pairs Lynparza with Piqray (alpelisib), a drug currently used to treat some patients with breast cancer. In an early trial of the combination that was reported in April 2019, 36% of patients had a partial response of some tumor shrinkage and half achieved stable disease, meaning their cancer didnt get worse. That was impressive, considering the bulk of the patients had become resistant to platinum chemotherapy, says Dr. Shannon Westin, a clinical investigator in the department of gynecologic oncology and reproductive medicine at MD Anderson. And there was a similar response rate regardless of mutation status, which was very exciting.

RESEARCHERS PURSUE MORE USES

Pairing PARP inhibitors with drugs that boost the immune systems ability to fight cancer is another idea being investigated in the treatment of ovarian cancer, because tumors with unstable DNA repair abilities might also be easier for the immune system to recognize. For example, Keytruda (pembrolizumab) inhibits programmed cell death protein 1 (PD-1), an immune checkpoint responsible for keeping the immune system under control.

The drug essentially takes the brakes off the immune system so it can better recognize and attack cancer. In an early trial combining Keytruda with Zejula, 65% of patients with ovarian cancer saw their disease come under control, either with total or partial tumor shrinkage or with stable disease.

Several other ongoing studies are combining PARP inhibition with immunotherapy, including a trial of Zejula with Tecentriq (atezolizumab), an inhibitor of a protein called programmed death-ligand 1 (PD-L1), and Cotellic (cobimetinib), which inhibits the cancer-associated mitogen-activated (MEK) protein. Another study combines Zejula with TSR-042, an investigational PD-1 blocker.

Could PARP inhibitors be useful for some women even earlier in the treatment process? MD Anderson recently started a small trial designed to investigate the potential of using the agents in place of chemotherapy in women with newly diagnosed cancer who have BRCA mutations. During the trial, patients will receive Lynparza for up to three months before moving on to surgery and chemotherapy. A similar trial is ongoing using the PARP inhibitor Talzenna (talazoparib) for BRCA-mutated breast cancer.

There could be many advantages of starting treatment with a PARP inhibitor rather than chemotherapy, Westin says. Patients can take the drugs at home instead of going to a facility for chemotherapy infusions. And PARP inhibitors dont cause many of the uncomfortable side effects common with chemotherapy, like neuropathy (numbness and tingling in the extremities) and hair loss. Some patients could potentially avoid that toxicity, Westin says.

The question is: Do we even need chemotherapy? Westin adds. Can we utilize a more targeted therapy to get better results? This is the next step.

Read more from the original source:
An Expanding Role For PARP Inhibitors Shows Promise In Treating Ovarian Cancer - Curetoday.com

An emergency room physician, initially unable to diagnose a disoriented patient, finds on the patient a wallet-sized card providing access to his genome, or all his DNA. The physician quickly searches the genome, diagnoses the problem and sends the patient off for a gene-therapy cure. Thats what a Pulitzer prize-winning journalist imagined 2020 would look like when she reported on the Human Genome Project back in 1996.

The Human Genome Project was an international scientific collaboration that successfully mapped, sequenced and made publicly available the genetic content of human chromosomes or all human DNA. Taking place between 1990 and 2003, the project caused many to speculate about the future of medicine. In 1996, Walter Gilbert, a Nobel laureate, said, The results of the Human Genome Project will produce a tremendous shift in the way we can do medicine and attack problems of human disease. In 2000, Francis Collins, then head of the HGP at the National Institutes of Health, predicted, Perhaps in another 15 or 20 years, you will see a complete transformation in therapeutic medicine. The same year, President Bill Clinton stated the Human Genome Project would revolutionize the diagnosis, prevention and treatment of most, if not all, human diseases.

It is now 2020 and no one carries a genome card. Physicians typically do not examine your DNA to diagnose or treat you. Why not? As I explain in a recent article in the Journal of Neurogenetics, the causes of common debilitating diseases are complex, so they typically are not amenable to simple genetic treatments, despite the hope and hype to the contrary.

The idea that a single gene can cause common diseases has been around for several decades. In the late 1980s and early 1990s, high-profile scientific journals, including Nature and JAMA, announced single-gene causation of bipolar disorder, schizophrenia and alcoholism, among other conditions and behaviors. These articles drew massive attention in the popular media, but were soon retracted or failed attempts at replication. These reevaluations completely undermined the initial conclusions, which often had relied on misguided statistical tests. Biologists were generally aware of these developments, though the follow-up studies received little attention in popular media.

There are indeed individual gene mutations that cause devastating disorders, such as Huntingtons disease. But most common debilitating diseases are not caused by a mutation of a single gene. This is because people who have a debilitating genetic disease, on average, do not survive long enough to have numerous healthy children. In other words, there is strong evolutionary pressure against such mutations. Huntingtons disease is an exception that endures because it typically does not produce symptoms until a patient is beyond their reproductive years. Although new mutations for many other disabling conditions occur by chance, they dont become frequent in the population.

Instead, most common debilitating diseases are caused by combinations of mutations in many genes, each having a very small effect. They interact with one another and with environmental factors, modifying the production of proteins from genes. The many kinds of microbes that live within the human body can play a role, too.

Since common serious diseases are rarely caused by single-gene mutations, they cannot be cured by replacing the mutated gene with a normal copy, the premise for gene therapy. Gene therapy has gradually progressed in research along a very bumpy path, which has included accidentally causing leukemia and at least one death, but doctors recently have been successful treating some rare diseases in which a single-gene mutation has had a large effect. Gene therapy for rare single-gene disorders is likely to succeed, but must be tailored to each individual condition. The enormous cost and the relatively small number of patients who can be helped by such a treatment may create insurmountable financial barriers in these cases. For many diseases, gene therapy may never be useful.

The Human Genome Project has had an enormous impact on almost every field of biological research, by spurring technical advances that facilitate fast, precise and relatively inexpensive sequencing and manipulation of DNA. But these advances in research methods have not led to dramatic improvements in treatment of common debilitating diseases.

Although you cannot bring your genome card to your next doctors appointment, perhaps you can bring a more nuanced understanding of the relationship between genes and disease. A more accurate understanding of disease causation may insulate patients against unrealistic stories and false promises.

[ Youre smart and curious about the world. So are The Conversations authors and editors. You can read us daily by subscribing to our newsletter. ]

See the article here:
Why sequencing the human genome failed to produce big breakthroughs in disease - The Conversation US

Naina Mishra

Tribune News Service

Chandigarh, February 14

The Post Graduate Institute of Medical Education and Research is in the process of developing a mobile-based application that will help patients to monitor asthma by identifying symptoms and personalised medication.

It is a two-year project in collaboration with the Ministry of Health, Government of India. The app will use a diagnostic and therapeutic algorithm to ascertain the personalised medicines for patients. The neural network in artificial intelligence (AI) will group patients in severe or mild category to personalise the treatment scheme.

Dr Anil Chauhan, who is associated with the project, said: A cohort of 10,000 records, as old as 20 years, of asthmatic children will be analysed through deep learning (a subset of artificial intelligence). The data will be incorporated in the electronic medical record so that a follow-up on the medical condition of every child can be managed easily.

Patients will be able to assess the mobile application and send reports of various tests such as pulmonary function tests (PFTs) or the asthma control test to the doctors concerned. Both doctors and patients will be able to view the medical history of the patient.

Through the database, we can see the types of changes required in treatment guidelines. Currently, the records of patients are being uploaded, said Chauhan.

Prof Meenu Singh, Department of Pediatrics, PGI, said: One medicine cannot be prescribed to all patients as there are different kinds of allergies. Precision medicine decides what kind of treatment will help every patient.

Precision medicine is an approach to patient care that allows doctors to select treatments that are most likely to help patients based on a genetic understanding of their disease.

All asthmatics dont react in the similar way to same drugs. The complications are so much that a poorly controlled asthma takes the form of allergic bronchopulmonary aspergillosis (ABPA), said Prof Meenu Singh, who is also a member of the Executive Committee, Indian Academy of Allergy, Congress Chair, IAACON 2020.

She added: So, we need to define these things while starting the therapy so that patients dont develop such complications. Precision medicine is helpful in such cases as there are certain genotypes that are more prone to such fungal response.

6,000 schoolchildren surveyed for asthma

The Global Asthma Network (GAN), established in 2012, has followed the International Study of Asthma and Allergies in Childhood (ISAAC). GAN phase 1 has been completed by the PGIMER for Chandigarh. There are nine centres in India contributing to the study.

All private and government schools of Chandigarh are part of the study. Children in the age group of 6 to 7 years and 12 to13 years were surveyed for asthma, wheezing and allergy. Around 6,000 children have been screened via set of questionnaires to develop the diagnostic algorithm.

The parents of these children were also screened as asthma is also genetic. Wheezing was found 8 per cent among children and asthma was found in 1-2 per cent. Wheezing is a high-pitched, coarse whistling sound you make when you breathe.

Link:
PGI coming up with mobile app to monitor asthma - The Tribune India

The institute is already carrying out research and it is the main centre not only in India, but in entire Asia.

New Delhi:The countrys premier All India Institute of Medical Sciences (AIIMS), Delhi, will sensitise people about the Celiac disease, which is spreading its tentacles among a large population. The disease is so far incurable and there is no medicine for it. Saturday was Celiac Day.The institute is already carrying out research and it is the main centre not only in India, but in entire Asia. It runs a special clinic for patients with Celiac disease every Thursday afternoon. So far 1,300 patients suffering from disease have been registered with the clinic.AIIMS Director Dr Randeep Guleria said, as per estimates, about 60-80 lakh Indians have Celiac disease, of them only a few have been diagnosed. With increasing awareness, the number of such patients will rise exponentially. There is a need to further increase the awareness about the disease and strengthen infrastructure for widespread availability of the diagnostic tests and also availability of reliable and affordable gluten-free food, he said.The disease occurs because of ingestion of a protein, called gluten, which is present in cereals like wheat and barley. This disease occurs only to those who have genetic susceptibility (presence of specific genes) which develops it. In these patients, gluten protein is not digested completely which leads to damage of the small intestine. Since food is not absorbed properly, patients fail to grow in height and weight, develop diarrhoea, anaemia and weakness of bones. They feel weak and thin.Speaking to this newspaper, Dr Govind Makharia said there is no treatment of the disease so far though the research is going on all over the world, including in AIIMS.The only way treatment is to avoid food products made of wheat and barley, which contains gluten. Early diagnosis is the key. Someone who is having regular complaints of diarrhoea, anemia should get himself diagnosed. It can be done through a blood test, he said.Earlier, he said, it was believed that the disease occurs only in children and seen only by paediatricians. But this is not true. Celiac disease can affect person of any age, including even elederly. Many a time, the patient many not have any obvious symptoms, but they fail to gain weight and their bones remain week and fracture even with minor trauma, he added.

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AIIMS to sensitise people on incurable Celiac - The Sunday Guardian

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Detailed genetic road map will guide research into TB treatments, vaccines

A new study led by Washington University School of Medicine in St. Louis lays out a genetic road map of immune responses to tuberculosis (TB) infection across three species. Pictured is a TB-infected human lung. TB is shown in green, and immune cells surrounding the TB bacteria are shown in red and white.

Tuberculosis (TB) is one of the worlds most vexing public health problems. About 1.5 million people died from this bacterial lung infection in 2018, and the World Health Organization (WHO) estimates that one-quarter of the worlds population some 2 billion people, mostly in developing countries are infected with the bacteria that causes TB.

For decades, scientists have been studying the deadly disease in mice and other animal models to develop drug therapies and vaccines to treat or prevent the infection. But findings in animals with TB dont always translate well to people with the disease, leaving scientists puzzled by the discrepancies.

Now, a new study led by Washington University School of Medicine in St. Louis offers a genetic road map detailing the similarities and differences in immune responses to TB across three species mice, macaques and humans. According to the researchers, the insight into the immune pathways that are activated in diverse models of TB infection will serve as a valuable tool for scientists studying and working to eradicate the disease.

The research, appearing Jan. 29 in the journal Science Translational Medicine, is a collaboration between Washington University; the Texas Biomedical Research Institute in San Antonio; and the University of Cape Town in South Africa.

For many years, scientists have been frustrated by the fact that animal models of TB especially the genetically identical mice so often studied dont really reflect what we see in people with TB infections, said co-senior author Shabaana A. Khader, PhD, a professor of molecular microbiology at Washington University. This study is important because now we show in great detail where these animal models overlap with humans with TB and where they dont.

Unlike many previous mouse studies, the new research involved genetically diverse mice that more closely recapitulate the wide range of TB infection severity in humans: Some infected individuals show no symptoms; others show intermediate degrees of severity; and still others develop extreme inflammation of the lungs.

With co-author Deepak Kaushal, PhD, at the Texas Biomedical Research Institute, the researchers compared the genetic and immune responses to TB infection in these diverse mice with the responses of TB-infected macaques in the Kaushal lab. And with co-author Thomas J. Scriba, PhD, of the University of Cape Town, the research team analyzed blood samples from adolescents in Western Cape, South Africa, who are enrolled in a clinical trial investigating TB infection. The samples from people allowed the researchers to analyze and compare data from the mice and macaques with a range of responses to TB infection in young people.

Past research from this long-running clinical trial identified a group of 16 genes whose activation patterns predicted the onset of TB disease more than a year before diagnosis. These genes called a human TB gene signature differed significantly in their activation patterns between young people who developed symptoms of TB and those who didnt.

In macaques, primates closely related to humans, scientists have long assumed that TB infection closely resembles such infection in people.

Our data demonstrate that 100% of the genes previously identified as a human TB gene signature overlap in macaques and people, said co-senior author Makedonka Mitreva, PhD, a professor of medicine and of genetics at Washington University and a researcher at the universitys McDonnell Genome Institute. Its important to have the definitive data showing it to be true.

There was significant overlap between humans and mice as well, according to the researchers, including co-first authors Mushtaq Ahmed, PhD, an assistant professor of molecular microbiology in Khaders lab; Shyamala Thirunavukkarasu, PhD, a staff scientist in Khaders lab; and Bruce A. Rosa, PhD, an assistant professor of medicine in Mitrevas lab. But they also identified genetic pathways that differed between mice and humans, providing detailed analysis of areas where TB in mice is unlikely to point to meaningful insight into human TB infection.

Until now, we have studied mouse models to understand TB disease progression, not knowing where the mouse disease translates to human disease and where it doesnt, Khader said. Now, we have shown that many areas do translate but that there are important aspects of TB infection that dont. If you are using mouse models to develop TB vaccines or other therapeutics that target areas that dont overlap, you likely wont succeed.

Added Mitreva, Our study will inform researchers when they may need to move to a different animal model to study their genetic or molecular pathways of interest.

The researchers studied in detail the genes that increase in expression in people who develop severe TB disease. Of 16 such genes identified in people, they were able to study 12 in mice. Four of the genes could not be studied because mice dont have equivalent versions of such genes or, when such genes were eliminated, the mouse embryos died during development.

The scientists found that the 12 genes fall into three categories: those that provide protection against TB infection; those that lead to greater susceptibility to TB infection; and those that had no effect either way. Such information will be useful in seeking future therapeutics that could, for example, boost effects of protective genes or shut down harmful ones.

According to Khader and Mitreva, their team plans to use the new knowledge to better understand TB infections that have become drug-resistant, a growing problem in places where the disease is endemic. In addition, they will harness the information to help understand why the TB vaccine often administered to high-risk groups of people works well in some individuals but not others.

With the studys raw data publicly available, Khader and Mitreva said they are hopeful it will serve as a valuable resource to TB research and immunology communities worldwide.

This work was supported by Washington University in St. Louis; the National Institutes of Health (NIH), grant numbers HL105427, AI111914-02, AI123780, AI134236-02, U19 AI91036 and U19AI106772; the Department of Molecular Microbiology at Washington University; and a Stephen I. Morse Fellowship; the Department of Medicine at the University of Rochester Medical Center.

Scriba is a co-inventor of a patent of the 16-gene signature for TB susceptibility from the Adolescent Cohort Study (ACS).

Washington University School of Medicines 1,500 faculty physicians also are the medical staff of Barnes-Jewish and St. Louis Childrens hospitals. The School of Medicine is a leader in medical research, teaching and patient care, ranking among the top 10 medical schools in the nation by U.S. News & World Report. Through its affiliations with Barnes-Jewish and St. Louis Childrens hospitals, the School of Medicine is linked to BJC HealthCare.

Read the rest here:
Immune responses to tuberculosis mapped across 3 species - Washington University School of Medicine in St. Louis

Meet Lea Starita, a Seattle-based genome scientist who is working to understand how our individual genes impact our health. Here, she answers some questions about her work.

What do you do? I am a research assistant professor of genome sciences at the University of Washington School of Medicine, and I co-direct the advanced technology lab at the Brotman Baty Institute for Precision Medicine (or the BAT-lab).

One of the main goals for precision medicine is to be able to practice genome-guided medicine. However, as a field, we are really good at reading DNA sequences of people, but we are really bad at understanding the health risks or benefits associated with any given DNA change. At the BAT lab, we are developing production-scale molecular-profiling technologies that we hope will accelerate our understanding of the impact of genetic variation on human development, human health and in treating disease.

The BATlab team also helped to build the worlds premier respiratory pathogen surveillance platform as part of the Seattle Flu Study.

How did you get started in this specialty?Ive been on this trajectory since I took an awesome molecular biology lab class in college. They handed us the New England Biolabs catalog to use instead of a textbook. To this day, that catalog contains nearly any enzyme you could need for cutting and pasting pieces of DNA together. I fell in love with the puzzle posed by molecular biology.

Whats a typical day like?I am lucky enough to get to spend the day with my colleagues, collaborators, staff and trainees who are all brilliant and creative scientists. My favorite times are when someone is at the white board drawing up a new idea or an improvement on an old idea. On the best days, I actually get in the lab to do some molecular biology myself. I love to play with DNA.

Whats the best part of the job?Dreaming up new technologies to answer tough biological questions with students, staff and collaborators. We try to answer questions like these: What is unique about each of the cell types in a human or animal? How do we understand the effect of a small change in a human or viral genome on health and disease? Although, I even find small process improvements exciting.

What surprises people about what you do? They are surprised when we talk about how important creativity and communication are in being successful as a scientist. I think people think we are these nerdy automatons, and that is totally not true. Well, the automaton part isnt true, anyway.

Do you have a cool job or know someone in the Seattle area who does? Email Michelle Archer with your recommendations for people to feature in Cool Job.

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Seattle-based genome scientist gets to play with DNA - Seattle Times