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Archive for the ‘Bio Instrumentation in Experimental Life Sciences Research’ Category

The Human Genome Gets Fully Sequenced: A Simplistic Take on Century Long Effort

 

Curator: Stephen J. Williams, PhD

Ever since the hard work by Rosalind Franklin to deduce structures of DNA and the coincidental work by Francis Crick and James Watson who modeled the basic building blocks of DNA, DNA has been considered as the basic unit of heredity and life, with the “Central Dogma” (DNA to RNA to Protein) at its core.  These were the discoveries in the early twentieth century, and helped drive the transformational shift of biological experimentation, from protein isolation and characterization to cloning protein-encoding genes to characterizing how the genes are expressed temporally, spatially, and contextually.

Rosalind Franklin, who’s crystolagraphic data led to determination of DNA structure. Shown as 1953 Time cover as Time person of the Year

Dr Francis Crick and James Watson in front of their model structure of DNA

 

 

 

 

 

 

 

 

 

Up to this point (1970s-mid 80s) , it was felt that genetic information was rather static, and the goal was still to understand and characterize protein structure and function while an understanding of the underlying genetic information was more important for efforts like linkage analysis of genetic defects and tools for the rapidly developing field of molecular biology.  But the development of the aforementioned molecular biology tools including DNA cloning, sequencing and synthesis, gave scientists the idea that a whole recording of the human genome might be possible and worth the effort.

How the Human Genome Project  Expanded our View of Genes Genetic Material and Biological Processes

 

 

From the Human Genome Project Information Archive

Source:  https://web.ornl.gov/sci/techresources/Human_Genome/project/hgp.shtml

History of the Human Genome Project

The Human Genome Project (HGP) refers to the international 13-year effort, formally begun in October 1990 and completed in 2003, to discover all the estimated 20,000-25,000 human genes and make them accessible for further biological study. Another project goal was to determine the complete sequence of the 3 billion DNA subunits (bases in the human genome). As part of the HGP, parallel studies were carried out on selected model organisms such as the bacterium E. coli and the mouse to help develop the technology and interpret human gene function. The DOE Human Genome Program and the NIH National Human Genome Research Institute (NHGRI) together sponsored the U.S. Human Genome Project.

 

Please see the following for goals, timelines, and funding for this project

 

History of the Project

It is interesting to note that multiple government legislation is credited for the funding of such a massive project including

Project Enabling Legislation

  • The Atomic Energy Act of 1946 (P.L. 79-585) provided the initial charter for a comprehensive program of research and development related to the utilization of fissionable and radioactive materials for medical, biological, and health purposes.
  • The Atomic Energy Act of 1954 (P.L. 83-706) further authorized the AEC “to conduct research on the biologic effects of ionizing radiation.”
  • The Energy Reorganization Act of 1974 (P.L. 93-438) provided that responsibilities of the Energy Research and Development Administration (ERDA) shall include “engaging in and supporting environmental, biomedical, physical, and safety research related to the development of energy resources and utilization technologies.”
  • The Federal Non-nuclear Energy Research and Development Act of 1974 (P.L. 93-577) authorized ERDA to conduct a comprehensive non-nuclear energy research, development, and demonstration program to include the environmental and social consequences of the various technologies.
  • The DOE Organization Act of 1977 (P.L. 95-91) mandated the Department “to assure incorporation of national environmental protection goals in the formulation and implementation of energy programs; and to advance the goal of restoring, protecting, and enhancing environmental quality, and assuring public health and safety,” and to conduct “a comprehensive program of research and development on the environmental effects of energy technology and program.”

It should also be emphasized that the project was not JUST funded through NIH but also Department of Energy

Project Sponsors

For a great read on Dr. Craig Ventnor with interviews with the scientist see Dr. Larry Bernstein’s excellent post The Human Genome Project

 

By 2003 we had gained much information about the structure of DNA, genes, exons, introns and allowed us to gain more insights into the diversity of genetic material and the underlying protein coding genes as well as many of the gene-expression regulatory elements.  However there was much uninvestigated material dispersed between genes, the then called “junk DNA” and, up to 2003 not much was known about the function of this ‘junk DNA’.  In addition there were two other problems:

  • The reference DNA used was actually from one person (Craig Ventor who was the lead initiator of the project)
  • Multiple gaps in the DNA sequence existed, and needed to be filled in

It is important to note that a tremendous amount of diversity of protein has been realized from both transcriptomic and proteomic studies.  Although about 20 to 25,000 coding genes exist the human proteome contains about 600,000 proteoforms (due to alternative splicing, posttranslational modifications etc.)

This expansion of the proteoform via alternate splicing into isoforms, gene duplication to paralogs has been shown to have major effects on, for example, cellular signaling pathways (1)

However just recently it has been reported that the FULL human genome has been sequenced and is complete and verified.  This was the focus of a recent issue in the journal Science.

Source: https://www.science.org/doi/10.1126/science.abj6987

Abstract

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

 

The current human reference genome was released by the Genome Reference Consortium (GRC) in 2013 and most recently patched in 2019 (GRCh38.p13) (1). This reference traces its origin to the publicly funded Human Genome Project (2) and has been continually improved over the past two decades. Unlike the competing Celera effort (3) and most modern sequencing projects based on “shotgun” sequence assembly (4), the GRC assembly was constructed from sequenced bacterial artificial chromosomes (BACs) that were ordered and oriented along the human genome by means of radiation hybrid, genetic linkage, and fingerprint maps. However, limitations of BAC cloning led to an underrepresentation of repetitive sequences, and the opportunistic assembly of BACs derived from multiple individuals resulted in a mosaic of haplotypes. As a result, several GRC assembly gaps are unsolvable because of incompatible structural polymorphisms on their flanks, and many other repetitive and polymorphic regions were left unfinished or incorrectly assembled (5).

 

Fig. 1. Summary of the complete T2T-CHM13 human genome assembly.
(A) Ideogram of T2T-CHM13v1.1 assembly features. For each chromosome (chr), the following information is provided from bottom to top: gaps and issues in GRCh38 fixed by CHM13 overlaid with the density of genes exclusive to CHM13 in red; segmental duplications (SDs) (42) and centromeric satellites (CenSat) (30); and CHM13 ancestry predictions (EUR, European; SAS, South Asian; EAS, East Asian; AMR, ad-mixed American). Bottom scale is measured in Mbp. (B and C) Additional (nonsyntenic) bases in the CHM13 assembly relative to GRCh38 per chromosome, with the acrocentrics highlighted in black (B) and by sequence type (C). (Note that the CenSat and SD annotations overlap.) RepMask, RepeatMasker. (D) Total nongap bases in UCSC reference genome releases dating back to September 2000 (hg4) and ending with T2T-CHM13 in 2021. Mt/Y/Ns, mitochondria, chrY, and gaps.

Note in Figure 1D the exponential growth in genetic information.

Also very important is the ability to determine all the paralogs, isoforms, areas of potential epigenetic regulation, gene duplications, and transposable elements that exist within the human genome.

Analyses and resources

A number of companion studies were carried out to characterize the complete sequence of a human genome, including comprehensive analyses of centromeric satellites (30), segmental duplications (42), transcriptional (49) and epigenetic profiles (29), mobile elements (49), and variant calls (25). Up to 99% of the complete CHM13 genome can be confidently mapped with long-read sequencing, opening these regions of the genome to functional and variational analysis (23) (fig. S38 and table S14). We have produced a rich collection of annotations and omics datasets for CHM13—including RNA sequencing (RNA-seq) (30), Iso-seq (21), precision run-on sequencing (PRO-seq) (49), cleavage under targets and release using nuclease (CUT&RUN) (30), and ONT methylation (29) experiments—and have made these datasets available via a centralized University of California, Santa Cruz (UCSC), Assembly Hub genome browser (54).

 

To highlight the utility of these genetic and epigenetic resources mapped to a complete human genome, we provide the example of a segmentally duplicated region of the chromosome 4q subtelomere that is associated with facioscapulohumeral muscular dystrophy (FSHD) (55). This region includes FSHD region gene 1 (FRG1), FSHD region gene 2 (FRG2), and an intervening D4Z4 macrosatellite repeat containing the double homeobox 4 (DUX4) gene that has been implicated in the etiology of FSHD (56). Numerous duplications of this region throughout the genome have complicated past genetic analyses of FSHD.

The T2T-CHM13 assembly reveals 23 paralogs of FRG1 spread across all acrocentric chromosomes as well as chromosomes 9 and 20 (Fig. 5A). This gene appears to have undergone recent amplification in the great apes (57), and approximate locations of FRG1 paralogs were previously identified by FISH (58). However, only nine FRG1 paralogs are found in GRCh38, hampering sequence-based analysis.

Future of the human reference genome

The T2T-CHM13 assembly adds five full chromosome arms and more additional sequence than any genome reference release in the past 20 years (Fig. 1D). This 8% of the genome has not been overlooked because of a lack of importance but rather because of technological limitations. High-accuracy long-read sequencing has finally removed this technological barrier, enabling comprehensive studies of genomic variation across the entire human genome, which we expect to drive future discovery in human genomic health and disease. Such studies will necessarily require a complete and accurate human reference genome.

CHM13 lacks a Y chromosome, and homozygous Y-bearing CHMs are nonviable, so a different sample type will be required to complete this last remaining chromosome. However, given its haploid nature, it should be possible to assemble the Y chromosome from a male sample using the same methods described here and supplement the T2T-CHM13 reference assembly with a Y chromosome as needed.

Extending beyond the human reference genome, large-scale resequencing projects have revealed genomic variation across human populations. Our reanalyses of the 1KGP (25) and SGDP (42) datasets have already shown the advantages of T2T-CHM13, even for short-read analyses. However, these studies give only a glimpse of the extensive structural variation that lies within the most repetitive regions of the genome assembled here. Long-read resequencing studies are now needed to comprehensively survey polymorphic variation and reveal any phenotypic associations within these regions.

Although CHM13 represents a complete human haplotype, it does not capture the full diversity of human genetic variation. To address this bias, the Human Pangenome Reference Consortium (59) has joined with the T2T Consortium to build a collection of high-quality reference haplotypes from a diverse set of samples. Ideally, all genomes could be assembled at the quality achieved here, but automated T2T assembly of diploid genomes presents a difficult challenge that will require continued development. Until this goal is realized, and any human genome can be completely sequenced without error, the T2T-CHM13 assembly represents a more complete, representative, and accurate reference than GRCh38.

 

This paper was the focus of a Time article and their basis for making the lead authors part of their Time 100 people of the year.

From TIME

The Human Genome Is Finally Fully Sequenced

Source: https://time.com/6163452/human-genome-fully-sequenced/

 

The first human genome was mapped in 2001 as part of the Human Genome Project, but researchers knew it was neither complete nor completely accurate. Now, scientists have produced the most completely sequenced human genome to date, filling in gaps and correcting mistakes in the previous version.

The sequence is the most complete reference genome for any mammal so far. The findings from six new papers describing the genome, which were published in Science, should lead to a deeper understanding of human evolution and potentially reveal new targets for addressing a host of diseases.

A more precise human genome

“The Human Genome Project relied on DNA obtained through blood draws; that was the technology at the time,” says Adam Phillippy, head of genome informatics at the National Institutes of Health’s National Human Genome Research Institute (NHGRI) and senior author of one of the new papers. “The techniques at the time introduced errors and gaps that have persisted all of these years. It’s nice now to fill in those gaps and correct those mistakes.”

“We always knew there were parts missing, but I don’t think any of us appreciated how extensive they were, or how interesting,” says Michael Schatz, professor of computer science and biology at Johns Hopkins University and another senior author of the same paper.

The work is the result of the Telomere to Telomere consortium, which is supported by NHGRI and involves genetic and computational biology experts from dozens of institutes around the world. The group focused on filling in the 8% of the human genome that remained a genetic black hole from the first draft sequence. Since then, geneticists have been trying to add those missing portions bit by bit. The latest group of studies identifies about an entire chromosome’s worth of new sequences, representing 200 million more base pairs (the letters making up the genome) and 1,956 new genes.

 

NOTE: In 2001 many scientists postulated there were as much as 100,000 coding human genes however now we understand there are about 20,000 to 25,000 human coding genes.  This does not however take into account the multiple diversity obtained from alternate splicing, gene duplications, SNPs, and chromosomal rearrangements.

Scientists were also able to sequence the long stretches of DNA that contained repeated sequences, which genetic experts originally thought were similar to copying errors and dismissed as so-called “junk DNA”. These repeated sequences, however, may play roles in certain human diseases. “Just because a sequence is repetitive doesn’t mean it’s junk,” says Eichler. He points out that critical genes are embedded in these repeated regions—genes that contribute to machinery that creates proteins, genes that dictate how cells divide and split their DNA evenly into their two daughter cells, and human-specific genes that might distinguish the human species from our closest evolutionary relatives, the primates. In one of the papers, for example, researchers found that primates have different numbers of copies of these repeated regions than humans, and that they appear in different parts of the genome.

“These are some of the most important functions that are essential to live, and for making us human,” says Eichler. “Clearly, if you get rid of these genes, you don’t live. That’s not junk to me.”

Deciphering what these repeated sections mean, if anything, and how the sequences of previously unsequenced regions like the centromeres will translate to new therapies or better understanding of human disease, is just starting, says Deanna Church, a vice president at Inscripta, a genome engineering company who wrote a commentary accompanying the scientific articles. Having the full sequence of a human genome is different from decoding it; she notes that currently, of people with suspected genetic disorders whose genomes are sequenced, about half can be traced to specific changes in their DNA. That means much of what the human genome does still remains a mystery.

The investigators in the Telomere to Telomere Consortium made the Time 100 People of the Year.

Michael Schatz, Karen Miga, Evan Eichler, and Adam Phillippy

Illustration by Brian Lutz for Time (Source Photos: Will Kirk—Johns Hopkins University; Nick Gonzales—UC Santa Cruz; Patrick Kehoe; National Human Genome Research Institute)

BY JENNIFER DOUDNA

MAY 23, 2022 6:08 AM EDT

Ever since the draft of the human genome became available in 2001, there has been a nagging question about the genome’s “dark matter”—the parts of the map that were missed the first time through, and what they contained. Now, thanks to Adam Phillippy, Karen Miga, Evan Eichler, Michael Schatz, and the entire Telomere-to-Telomere Consortium (T2T) of scientists that they led, we can see the full map of the human genomic landscape—and there’s much to explore.

In the scientific community, there wasn’t a consensus that mapping these missing parts was necessary. Some in the field felt there was already plenty to do using the data in hand. In addition, overcoming the technical challenges to getting the missing information wasn’t possible until recently. But the more we learn about the genome, the more we understand that every piece of the puzzle is meaningful.

I admire the

T2T group’s willingness to grapple with the technical demands of this project and their persistence in expanding the genome map into uncharted territory. The complete human genome sequence is an invaluable resource that may provide new insights into the origin of diseases and how we can treat them. It also offers the most complete look yet at the genetic script underlying the very nature of who we are as human beings.

Doudna is a biochemist and winner of the 2020 Nobel Prize in Chemistry

Source: https://time.com/collection/100-most-influential-people-2022/6177818/evan-eichler-karen-miga-adam-phillippy-michael-schatz/

Other articles on the Human Genome Project and Junk DNA in this Open Access Scientific Journal Include:

 

International Award for Human Genome Project

 

Cracking the Genome – Inside the Race to Unlock Human DNA – quotes in newspapers

 

The Human Genome Project

 

Junk DNA and Breast Cancer

 

A Perspective on Personalized Medicine

 

 

 

 

 

 

 

Additional References

 

  1. P. Scalia, A. Giordano, C. Martini, S. J. Williams, Isoform- and Paralog-Switching in IR-Signaling: When Diabetes Opens the Gates to Cancer. Biomolecules 10, (Nov 30, 2020).

 

 

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Embryogenesis in Mechanical Womb

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

A highly effective platforms for the ex utero culture of post-implantation mouse embryos have been developed in the present study by scientists of the Weizmann Institute of Science in Israel. The study was published in the journal Nature. They have grown more than 1,000 embryos in this way. This study enables the appropriate development of embryos from before gastrulation (embryonic day (E) 5.5) until the hindlimb formation stage (E11). Late gastrulating embryos (E7.5) are grown in three-dimensional rotating bottles, whereas extended culture from pre-gastrulation stages (E5.5 or E6.5) requires a combination of static and rotating bottle culture platforms.

At Day 11 of development more than halfway through a mouse pregnancy the researchers compared them to those developing in the uteruses of living mice and were found to be identical. Histological, molecular and single-cell RNA sequencing analyses confirm that the ex utero cultured embryos recapitulate in utero development precisely. The mouse embryos looked perfectly normal. All their organs developed as expected, along with their limbs and circulatory and nervous systems. Their tiny hearts were beating at a normal 170 beats per minute. But, the lab-grown embryos becomes too large to survive without a blood supply. They had a placenta and a yolk sack, but the nutrient solution that fed them through diffusion was no longer sufficient. So, a suitable mechanism for blood supply is required to be developed.

Till date the only way to study the development of tissues and organs is to turn to species like worms, frogs and flies that do not need a uterus, or to remove embryos from the uteruses of experimental animals at varying times, providing glimpses of development more like in snapshots than in live videos. This research will help scientists understand how mammals develop and how gene mutations, nutrients and environmental conditions may affect the fetus. This will allow researchers to mechanistically interrogate post-implantation morphogenesis and artificial embryogenesis in mammals. In the future it may be possible to develop a human embryo from fertilization to birth entirely outside the uterus. But the work may one day raise profound questions about whether other animals, even humans, should or could be cultured outside a living womb.

References:

https://www.nature.com/articles/s41586-021-03416-3

https://www.sciencedirect.com/science/article/pii/S0092867414000750?via%3Dihub

https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1469-185X.1978.tb00993.x

https://www.nature.com/articles/199297a0

https://rep.bioscientifica.com/view/journals/rep/35/1/jrf_35_1_018.xml

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National Resilience, Inc. is a first-of-its-kind manufacturing and technology company dedicated to broadening access to complex medicines and protecting biopharmaceutical supply chains against disruption – the Acquisition of Two Premier Biologics Manufacturing Facilities: Boston and in Ontario, Canada

 

Reporter: Aviva Lev-Ari, PhD, RN

Resilience’s new facility, located at 500 Soldiers Field Rd., Boston, MA. (Photo: Business Wire) – The Genzyme-Sanofi Building

 

SAN DIEGO & BOSTON–(BUSINESS WIRE)–Resilience (National Resilience, Inc.), a new company building the world’s most advanced biopharmaceutical manufacturing ecosystem, announced it has acquired two premier commercial manufacturing facilities in North America, joining other facilities already in Resilience’s network to boost total capacity under management to more than 750,000 square feet.

“These locations will serve as hubs for the future of biopharma manufacturing, leading the way and shaping the future of Resilience.”

  • The acquired facilities include a 310,000-square-foot plant in Boston, MA, purchased from Sanofi; and in a separate transaction,
  • a 136,000-square-foot plant in Mississauga, Ontario, Canada.

Both facilities, which currently produce commercial, marketed products, will see significant investments as Resilience adds capacity and capabilities to produce new therapies at these locations. In addition, the company has offered employment to the existing plant staff and intends to add more jobs at each facility.

“We have big plans for these facilities including investing in new capacity, applying new manufacturing technologies, creating jobs and bringing in new customers,” said Rahul Singhvi, Sc.D, Chief Executive Officer of Resilience. “These locations will serve as hubs for the future of biopharma manufacturing, leading the way and shaping the future of Resilience.”

As part of its agreement with Sanofi, Resilience will continue to manufacture a marketed product at the Boston location. The facility plan includes a build out to facilitate multi-modality manufacturing and state-of-the-art quality laboratories to ensure safe, reliable supply to patients. The facility itself is certified ISO 14001 (Environmental management system), OSHAS 18001 (Health & safety management system) and ISO 50001 (Energy management system).​

This is currently the largest of several facilities in Resilience’s growing biologics and advanced therapeutics manufacturing network, with plans to acquire and develop other sites in the U.S. this year. The facility offers 24/7/365 production, multiple 2000L bioreactors capacity and multiple downstream processing trains, with investment in additional capabilities to come.

Our state-of-the-art flexible facility in Mississauga, Ontario, provides upstream, downstream and aseptic fill finish, and is designed to comply with cGMP. The plant has been inspected and approved by multiple regulatory bodies, and handles development and commercialized products.

About Resilience

Resilience (National Resilience, Inc.) is a first-of-its-kind manufacturing and technology company dedicated to broadening access to complex medicines and protecting biopharmaceutical supply chains against disruption. Founded in 2020, the company is building a sustainable network of high-tech, end-to-end manufacturing solutions to ensure the medicines of today and tomorrow can be made quickly, safely, and at scale. Resilience offers the highest quality and regulatory capabilities, and flexible and adaptive facilities to serve partners of all sizes. By continuously advancing the science of biopharmaceutical manufacturing and development, Resilience frees partners to focus on the discoveries that improve patients’ lives.

For more information, visit www.Resilience.com.

Contacts

Ryan Flinn
Head of Communications
Ryan.flinn@Resilience.com
510-207-7616

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Life-changing surgical blade technology to enhance patient healing

Reporter: Irina Robu, PhD

Entrepix Medical, a US based start-up specializes in applying nano-polishing technology introduced a new life-changing surgical blade technology considered to advance patient healing. The start-up claims its Planatome technology which applies a patented nano-polishing process to erase manufacturing defects found on standard scalpels and gives the surgical instruments an ultra-smooth and consistent cutting surface.

According to Entrepix Medical, their surgical blade technology improves pos-procedures outcome including faster healing, increase wound strength, minimizes chances of infections, less pain, less scaring and reduced nerve damage.  Their studies have shown wound closure rates from incisions made using Planatome technology can be larger than 90 percent after 24 hours, compared to 10% attained by traditional scalpels.

Entrepix Medical studies show that nerves incised with a Planatome blade demonstrated 25% recovery five weeks after surgery, while a nerve cut with a standard scalpel showed a 9% recovery and after 12 weeks, the nerves incised with a Planatome blade showed a 92% recovery.

Planatome Technology by Entrepix Medical reevaluates surgical potentials for both the surgeon and patient by familiarizing the most advanced nano-polishing technology used in microchip manufacturing and applying it to surgical instruments. A Planatome blade is the only surgical instrument of its kind that provides the atomic level precision and consistency required to minimize these possible difficulties.

SOURCE

https://www.nsmedicaldevices.com/news/entrepix-medical-planatome

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Biomolecular Condensates: A new approach to biology originated @MIT – Drug Discovery at DewPoint Therapeutics, Cambridge, MA gets new leaders, Ameet Nathwani, MD (ex-Sanofi, ex-Novartis) as Chief Executive Officer and Arie Belldegrun, PhD (ex-Kite Therapeutics) on R&D

Curator & Reporter: Aviva Lev-Ari, PhD, RN

 

Hooked by the science, Arie Belldegrun joins a group of influentials who believe Dewpoint may have the key to the next big thing in biotech

A new approach to biology

“The real voyage of discovery consists, not in seeking new landscapes, but in having new eyes.” Marcel Proust

Starting with the study of P granules in C.elegans embryos in 2009, Tony Hyman, working with his collaborators like Frank Julicher, Cliff Brangwynne, Simon Alberti, Mike Rosen, and Rohit Pappu, began to unravel the mysteries of biomolecular condensates. These scientists realized that P granules behave like liquid droplets that form by phase separation (think of oil droplets in salad dressing) and called them condensates.

In subsequent studies, they found to their surprise that many compartments inside cells had the behavior of condensates: they are liquid-like and form by phase separation.

Inspired by the work of Tony and his colleagues, Richard Young, Phillip Sharp, and Arup Chakraborty at MIT applied these approaches to the study of gene expression, similarly shedding light on many important questions in gene control.

a video thumbnail

 

Press releases and Dewpoint in the news

 
  • Dewpoint Therapeutics Appoints Ameet Nathwani as Chief Executive Officer

    Dewpoint

  • New York Times interviews Rick Young and Amy Gladfelter on the role of condensate “droplets” in COVID-19

    New York Times

  • Dewpoint Therapeutics raises $77 million to go after ‘undruggable’ diseases

    Boston Globe

  • Hooked by the science, Arie Belldegrun joins a group of influentials who believe Dewpoint may have the key to the next big thing in biotech

    Endpoint News

  • Dewpoint Therapeutics to put ‘pedal to the metal’ with $77M round

    FierceBiotech

  • Dewpoint Therapeutics Raises $77M Series B Financing to Advance the Development of Drugs That Target Biomolecular Condensates

    Dewpoint

  • 21 biotech startups that are set to take off, according to top VCs

    Business Insider

  • Proteins — and labs — coming together to prevent Rett Syndrome

    Whitehead Institute

  • Dewpoint Therapeutics Collaborates with Merck to Evaluate Novel Approach for the Treatment of HIV

    Dewpoint

  • Discovery of how cancer drugs find their targets could lead to a new toolset for drug development

    Whitehead Institute

SOURCE

https://dewpointx.com/news/

Other related article published in this Online Open Access Scientific Journal include: 

Economic Potential of a Drug Invention (Prof. Zelig Eshhar, Weitzman Institute, registered the patent) versus a Cancer Drug in Clinical Trials: CAR-T as a Case in Point, developed by Kite Pharma, under Arie Belldegrun, CEO, acquired by Gilead for $11.9 billion, 8/2017.

https://pharmaceuticalintelligence.com/2017/10/04/economic-potential-of-a-drug-invention-prof-zelig-eshhar-weitzman-institute-registered-the-patent-versus-a-cancer-drug-in-clinical-trials-car-t-as-a-case-in-point-developed-by-kite-pharma-unde/

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Medicine in 2045 – Perspectives by World Thought Leaders in the Life Sciences & Medicine

Reporter: Aviva Lev-Ari, PhD, RN

 

This report is based on an article in Nature Medicine | VOL 25 | December 2019 | 1800–1809 | http://www.nature.com/naturemedicine

Looking forward 25 years: the future of medicine.

Nat Med 25, 1804–1807 (2019) doi:10.1038/s41591-019-0693-y

 

Aviv Regev, PhD

Core member and chair of the faculty, Broad Institute of MIT and Harvard; director, Klarman Cell Observatory, Broad Institute of MIT and Harvard; professor of biology, MIT; investigator, Howard Hughes Medical Institute; founding co-chair, Human Cell Atlas.

  • millions of genome variants, tens of thousands of disease-associated genes, thousands of cell types and an almost unimaginable number of ways they can combine, we had to approximate a best starting point—choose one target, guess the cell, simplify the experiment.
  • In 2020, advances in polygenic risk scores, in understanding the cell and modules of action of genes through genome-wide association studies (GWAS), and in predicting the impact of combinations of interventions.
  • we need algorithms to make better computational predictions of experiments we have never performed in the lab or in clinical trials.
  • Human Cell Atlas and the International Common Disease Alliance—and in new experimental platforms: data platforms and algorithms. But we also need a broader ecosystem of partnerships in medicine that engages interaction between clinical experts and mathematicians, computer scientists and engineers

Feng Zhang, PhD

investigator, Howard Hughes Medical Institute; core member, Broad Institute of MIT and Harvard; James and Patricia Poitras Professor of Neuroscience, McGovern Institute for Brain Research, MIT.

  • fundamental shift in medicine away from treating symptoms of disease and toward treating disease at its genetic roots.
  • Gene therapy with clinical feasibility, improved delivery methods and the development of robust molecular technologies for gene editing in human cells, affordable genome sequencing has accelerated our ability to identify the genetic causes of disease.
  • 1,000 clinical trials testing gene therapies are ongoing, and the pace of clinical development is likely to accelerate.
  • refine molecular technologies for gene editing, to push our understanding of gene function in health and disease forward, and to engage with all members of society

Elizabeth Jaffee, PhD

Dana and Albert “Cubby” Broccoli Professor of Oncology, Johns Hopkins School of Medicine; deputy director, Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins.

  • a single blood test could inform individuals of the diseases they are at risk of (diabetes, cancer, heart disease, etc.) and that safe interventions will be available.
  • developing cancer vaccines. Vaccines targeting the causative agents of cervical and hepatocellular cancers have already proven to be effective. With these technologies and the wealth of data that will become available as precision medicine becomes more routine, new discoveries identifying the earliest genetic and inflammatory changes occurring within a cell as it transitions into a pre-cancer can be expected. With these discoveries, the opportunities to develop vaccine approaches preventing cancers development will grow.

Jeremy Farrar, OBE FRCP FRS FMedSci

Director, Wellcome Trust.

  • shape how the culture of research will develop over the next 25 years, a culture that cares more about what is achieved than how it is achieved.
  • building a creative, inclusive and open research culture will unleash greater discoveries with greater impact.

John Nkengasong, PhD

Director, Africa Centres for Disease Control and Prevention.

  • To meet its health challenges by 2050, the continent will have to be innovative in order to leapfrog toward solutions in public health.
  • Precision medicine will need to take center stage in a new public health order— whereby a more precise and targeted approach to screening, diagnosis, treatment and, potentially, cure is based on each patient’s unique genetic and biologic make-up.

Eric Topol, MD

Executive vice-president, Scripps Research Institute; founder and director, Scripps Research Translational Institute.

  • In 2045, a planetary health infrastructure based on deep, longitudinal, multimodal human data, ideally collected from and accessible to as many as possible of the 9+ billion people projected to then inhabit the Earth.
  • enhanced capabilities to perform functions that are not feasible now.
  • AI machines’ ability to ingest and process biomedical text at scale—such as the corpus of the up-to-date medical literature—will be used routinely by physicians and patients.
  • the concept of a learning health system will be redefined by AI.

Linda Partridge, PhD

Professor, Max Planck Institute for Biology of Ageing.

  • Geroprotective drugs, which target the underlying molecular mechanisms of ageing, are coming over the scientific and clinical horizons, and may help to prevent the most intractable age-related disease, dementia.

Trevor Mundel, MD

President of Global Health, Bill & Melinda Gates Foundation.

  • finding new ways to share clinical data that are as open as possible and as closed as necessary.
  • moving beyond drug donations toward a new era of corporate social responsibility that encourages biotechnology and pharmaceutical companies to offer their best minds and their most promising platforms.
  • working with governments and multilateral organizations much earlier in the product life cycle to finance the introduction of new interventions and to ensure the sustainable development of the health systems that will deliver them.
  • deliver on the promise of global health equity.

Josep Tabernero, MD, PhD

Vall d’Hebron Institute of Oncology (VHIO); president, European Society for Medical Oncology (2018–2019).

  • genomic-driven analysis will continue to broaden the impact of personalized medicine in healthcare globally.
  • Precision medicine will continue to deliver its new paradigm in cancer care and reach more patients.
  • Immunotherapy will deliver on its promise to dismantle cancer’s armory across tumor types.
  • AI will help guide the development of individually matched
  • genetic patient screenings
  • the promise of liquid biopsy policing of disease?

Pardis Sabeti, PhD

Professor, Harvard University & Harvard T.H. Chan School of Public Health and Broad Institute of MIT and Harvard; investigator, Howard Hughes Medical Institute.

  • the development and integration of tools into an early-warning system embedded into healthcare systems around the world could revolutionize infectious disease detection and response.
  • But this will only happen with a commitment from the global community.

Els Toreele, PhD

Executive director, Médecins Sans Frontières Access Campaign

  • we need a paradigm shift such that medicines are no longer lucrative market commodities but are global public health goods—available to all those who need them.
  • This will require members of the scientific community to go beyond their role as researchers and actively engage in R&D policy reform mandating health research in the public interest and ensuring that the results of their work benefit many more people.
  • The global research community can lead the way toward public-interest driven health innovation, by undertaking collaborative open science and piloting not-for-profit R&D strategies that positively impact people’s lives globally.

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Real Time Coverage of BIO 2019 International Convention, June 3-6, 2019 Philadelphia Convention Center, Philadelphia PA

Reporter: Stephen J. Williams, PhD @StephenJWillia2

Please follow LIVE on TWITTER using the following @ handles and # hashtags:

@Handles

@pharma_BI

@AVIVA1950

@BIOConvention

# Hashtags

#BIO2019 (official meeting hashtag)

Please check daily on this OPEN ACCESS JOURNAL for updates on one of the most important BIO Conferences of the year for meeting notes, posts, as well as occasional PODCASTS.

 

The BIO International Convention is the largest global event for the biotechnology industry and attracts the biggest names in biotech, offers key networking and partnering opportunities, and provides insights and inspiration on the major trends affecting the industry. The event features keynotes and sessions from key policymakers, scientists, CEOs, and celebrities.  The Convention also features the BIO Business Forum (One-on-One Partnering), hundreds of sessions covering biotech trends, policy issues and technological innovations, and the world’s largest biotechnology exhibition – the BIO Exhibition.

The BIO International Convention is hosted by the Biotechnology Innovation Organization (BIO). BIO represents more than 1,100 biotechnology companies, academic institutions, state biotechnology centers and related organizations across the United States and in more than 30 other nations. BIO members are involved in the research and development of innovative healthcare, agricultural, industrial and environmental biotechnology products.

 

Keynote Speakers INCLUDE:

Fireside Chat with Margaret (Peggy) Hamburg, MD, Foreign Secretary, National Academy of Medicine; Chairman of the Board, American Association for the Advancement of Science

Tuesday Keynote: Siddhartha Mukherjee (Author of the bestsellers Emperor of All Maladies: A Biography of Cancer and  The Gene: An Intimate History)

Fireside Chat with Jeffrey Solomon, Chief Executive Officer, COWEN

Fireside Chat with Christi Shaw, Senior Vice President and President, Lilly BIO-Medicines, Eli Lilly and Company

Wednesday Keynote: Jamie Dimon (Chairman JP Morgan Chase)

Fireside Chat with Kenneth C. Frazier, Chairman of the Board and Chief Executive Officer, Merck & Co., Inc.

Fireside Chat: Understanding the Voices of Patients: Unique Perspectives on Healthcare

Fireside Chat: FDA Town Hall

 

ALSO SUPERSESSIONS including:

Super Session: What’s Next: The Landscape of Innovation in 2019 and Beyond

Super Session: Falling in Love with Science: Championing Science for Everyone, Everywhere

Super Session: Digital Health in Practice: A Conversation with Ameet Nathawani, Chief Digital Officer, Chief Medical Falling in Love with Science: Championing Science for Everyone, Everywhere

Super Session: Realizing the Promise of Gene Therapies for Patients Around the World

Super Session: Biotech’s Contribution to Innovation: Current and Future Drivers of Success

Super Session: The Art & Science of R&D Innovation and Productivity

Super Session: Dealmaker’s Intentions: 2019 Market Outlook

Super Session: The State of the Vaccine Industry: Stimulating Sustainable Growth

 

See here for full AGENDA

Link for Registration: https://convention.bio.org/register/

The BIO International Convention is literally where hundreds of deals and partnerships have been made over the years.

 

BIO performs many services for members, but none of them are more visible than the BIO International Convention. The BIO International Convention helps BIO fulfill its mission to help grow the global biotech industry. Profits from the BIO International Convention are returned to the biotechnology industry by supporting BIO programs and initiatives. BIO works throughout the year to create a policy environment that enables the industry to continue to fulfill its vision of bettering the world through biotechnology innovation.

The key benefits of attending the BIO International Convention are access to global biotech and pharma leaders via BIO One-on-One Partnering, exposure to industry though-leaders with over 1,500 education sessions at your fingertips, and unparalleled networking opportunities with 16,000+ attendees from 74 countries.

In addition, we produce BIOtechNOW, an online blog chronicling ‘innovations transforming our world’ and the BIO Newsletter, the organization’s bi-weekly email newsletter. Subscribe to the BIO Newsletter.

 

Membership with the Biotechnology Innovation Organization (BIO)

BIO has a diverse membership that is comprised of  companies from all facets of biotechnology. Corporate R&D members range from entrepreneurial companies developing a first product to Fortune 100 multinationals. The majority of our members are small companies – 90 percent have annual revenues of $25 million or less, reflecting the broader biotechnology industry. Learn more about how you can save with BIO Membership.

BIO also represents academic centers, state and regional biotech associations and service providers to the industry, including financial and consulting firms.

  • 66% R&D-Intensive Companies *Of those: 89% have annual revenues under $25 million,  4% have annual revenues between $25 million and $1 billion, 7% have annual revenues over $1 billion.
  • 16% Nonprofit/Academic
  • 11% Service Providers
  • 7% State/International Affiliate Organizations

Other posts on LIVE CONFERENCE COVERAGE using Social Media on this OPEN ACCESS JOURNAL and OTHER Conferences Covered please see the following link at https://pharmaceuticalintelligence.com/press-coverage/

 

Notable Conferences Covered THIS YEAR INCLUDE: (see full list from 2013 at this link)

  • Koch Institute 2019 Immune Engineering Symposium, January 28-29, 2019, Kresge Auditorium, MIT

https://calendar.mit.edu/event/immune_engineering_symposium_2019#.XBrIDc9Kgcg

http://kochinstituteevents.cvent.com/events/koch-institute-2019-immune-engineering-symposium/event-summary-8d2098bb601a4654991060d59e92d7fe.aspx?dvce=1

 

  • 2019 MassBio’s Annual Meeting, State of Possible Conference ​, March 27 – 28, 2019, Royal Sonesta, Cambridge

http://files.massbio.org/file/MassBio-State-Of-Possible-Conference-Agenda-Feb-22-2019.pdf

 

  • World Medical Innovation Forum, Partners Innovations, ARTIFICIAL INTELLIGENCE | APRIL 8–10, 2019 | Westin, BOSTON

https://worldmedicalinnovation.org/agenda-list/

https://worldmedicalinnovation.org/

 

  • 18th Annual 2019 BioIT, Conference & Expo, April 16-18, 2019, Boston, Seaport World Trade Center, Track 5 Next-Gen Sequencing Informatics – Advances in Large-Scale Computing

http://www.giiconference.com/chi653337/

https://pharmaceuticalintelligence.com/2019/04/22/18th-annual-2019-bioit-conference-expo-april-16-18-2019-boston-seaport-world-trade-center-track-5-next-gen-sequencing-informatics-advances-in-large-scale-computing/

 

  • Translating Genetics into Medicine, April 25, 2019, 8:30 AM – 6:00 PM, The New York Academy of Sciences, 7 World Trade Center, 250 Greenwich St Fl 40, New York

https://pharmaceuticalintelligence.com/2019/04/25/translating-genetics-into-medicine-april-25-2019-830-am-600-pm-the-new-york-academy-of-sciences-7-world-trade-center-250-greenwich-st-fl-40-new-york/

 

  • 13th Annual US-India BioPharma & Healthcare Summit, May 9, 2019, Marriott, Cambridge

https://pharmaceuticalintelligence.com/2019/04/30/13th-annual-biopharma-healthcare-summit-thursday-may-9-2019/

 

  • 2019 Petrie-Flom Center Annual Conference: Consuming Genetics: Ethical and Legal Considerations of New Technologies, May 17, 2019, Harvard Law School

http://petrieflom.law.harvard.edu/events/details/2019-petrie-flom-center-annual-conference

https://pharmaceuticalintelligence.com/2019/01/11/2019-petrie-flom-center-annual-conference-consuming-genetics-ethical-and-legal-considerations-of-new-technologies/

 

  • 2019 Koch Institute Symposium – Machine Learning and Cancer, June 14, 2019, 8:00 AM-5:00 PM  ET MIT Kresge Auditorium, 48 Massachusetts Ave, Cambridge, MA

https://pharmaceuticalintelligence.com/2019/03/12/2019-koch-institute-symposium-machine-learning-and-cancer-june-14-2019-800-am-500-pmet-mit-kresge-auditorium-48-massachusetts-ave-cambridge-ma/

 

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Updated 70/16/2020

In this article, they review the past applications of in vitro models in identifying human hepatotoxins and focus on the use of multiscale experimental models in drug development, including the use of zebrafish and human cell-based, 3-dimensional (3D), microfluidic systems of liver functions as key components in applying Quantitative Systems
Pharmacology (QSP). They have implemented QSP as a platform to improve the rate of success in the process of drug discovery and development of therapeutics.

The stakeholders involved in drug development from academia, industry, and government agencies know the need to improve drug candidate selection by optimizing efficacy while screening out potential toxins so as to concentrate efforts with favorable chances for market approval. A survey of the number of new drugs released between 2000 and 2009 demonstrated a 25-year low in drug approvals despite increases in research and development (R&D) investment.

SOURCE

Click to access nihms-1002432.pdf

Lab on a chip Enters a New Field

Reporter: Irina Robu, PhD

The basis of the lab-on-a-chip is to integrate thousands of biochemical operations onto a single chip that could be done by splitting a single drop of blood collected from the patient in order to get a precise diagnosis of potential diseases. Research on lab-on-a-chip primarily focuses on human diagnostics and DNA analysis. Miniaturization of biochemical operations normally handled in a laboratory has numerous advantages, such as cost efficiency, diagnostic speed and sensitivity. The emergence of the lab-on-a-chip field mainly relies on two core technologies: microfluidics and molecular biology.

The team led by Govind Kaigala at IBM Research-Zurich and the group of Moran Bercovici at Technion-Israel Institute of Technology designed a new device that can effectively control liquids and materials on the micro-scale and have demonstrated that the key to dynamic control of fluid mechanics may be electric. Their research is published on Proceedings of the National Academy of Sciences.

The research team turned to electric field to control the control the motion of fluid in a way that is adjustable. When liquid contacts a surface, it develops a layer of charge; applying an electric field to this layer moves the charges, dragging the liquid with them and creating a net flow.

Using this knowledge, the team calculated a device that uses disk-shaped electrodes implanted in the bottom of a fluidic chamber to produce dipole-like flow patterns in the liquid when an electric field is applied. Placing multiple electrodes together in an array generates “virtual channels” that guide the fluid stream. By altering the voltages on the electrodes, they could then reverse the pattern to create an inner region of flow bounded by an outer region of stagnation, which is useful for selective on-demand mixing. While more applications of these flow patterns have yet to be explored, the control and flexibility the team’s device offers recommend that the lab-on-a-chip dream may finally be within grasp.

SOURCE

https://physicsworld.com/a/microfluidics-enters-a-new-field/

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Print’s Technology Used to Help Produce 3D Printed Glass Molds for Droplet Microfluidic Chips

Reporter: Irina Robu, PhD

Scientists from Leibniz HKI, Friedrich Schiller University, the Ilmenau University of Technology, FEMTOprint  and the Fraunhofer Institute for Applied Optics and Precision Engineering fabricated 3D polydimethylsiloxane (PDMS) chips for droplet microfluidics by using FEMTOprint’s innovative glass technology to make 3D printed glass molds. The 3D printed glass mold can pack 192 nozzles into a design that’s 25 mm long and 4 mm wide, including all inlets and outlets, which produce monodisperse droplets of 70 µm. It’s also easy to scale this structure so it is capable of holding 1,000 nozzles in a 6.5 cm structure.

FEMTOprint’s direct writing process makes it possible to produce microfluidic designs with diverse levels, continuously changing heights, and complex 3D shapes, along with sub-micrometric resolution. 3D printed glass molds are used to combine the replication and ease of production that soft lithography is capable of with the advantages of high-resolution prototyping. Moreover, it can facilitate fabrication of multilevel structures even ones with gradients of confinement, which can make important droplet microfluidic operations better.

This technique, paired with simple polydimethylsiloxane replica molding, can offer users with a solution for non-specialized and specialized labs in order to customize and expand microfluidic experimentation. In order to leverage the immense potential of droplet microfluidics, the process of chip design and fabrication needs to be simplified. While the PDMS replica molding has significantly transformed the chip-production process, its dependence on 2D-limited photolithography has limited the design possibilities, as well as further dissemination of microfluidics to non-specialized labs. The technique permits new possibilities in the university, meanwhile as of right now, no other methodology exists except this one that allows architectures with structures from 15 µm to hundreds of micrometers in all dimensions to be produced.

According to FEMTOprint, 3D printed glass structures characterize a negative part, and can be used as chips by bonding them to a PDMS slab or glass, which makes it possible to utilize structures, like mirrors, lenses, and filters, that replica molding cannot recreate. Chip fabrication doesn’t have to be the holdup for non-microfluidic labs adopting microfluidic approaches, instead it should be looked at as a way to device novel functionalities, like optical fiber incorporation for fluorescence detection.

 SOURCE

https://www.industrial-lasers.com/articles/2018/07/3d-printing-creates-molds-for-droplet-microfluidic-chips.html

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UPDATED on 12/26/2020 – CABG: a Superior Revascularization Modality to PCI in Patients with poor LVF, Multivessel disease and Diabetes, Similar Risk of Stroke between 31 days and 5 years, post intervention

Reporter: Aviva Lev-Ari, PhD, RN

 

UPDATED on 12/26/2020

Five-Year Outcomes after PCI or CABG for Left Main Coronary Disease

List of authors.

  • Gregg W. Stone, M.D.,
  • A. Pieter Kappetein, M.D., Ph.D.,
  • Joseph F. Sabik, M.D.,
  • Stuart J. Pocock, Ph.D.,
  • Marie-Claude Morice, M.D.,
  • John Puskas, M.D.,
  • David E. Kandzari, M.D.,
  • Dimitri Karmpaliotis, M.D.,
  • W. Morris Brown, III, M.D.,
  • Nicholas J. Lembo, M.D.,
  • Adrian Banning, M.D.,
  • Béla Merkely, M.D.,
  • et al.,
  •  for the EXCEL Trial Investigators*

Abstract

BACKGROUND

Long-term outcomes after percutaneous coronary intervention (PCI) with contemporary drug-eluting stents, as compared with coronary-artery bypass grafting (CABG), in patients with left main coronary artery disease are not clearly established.

METHODS

We randomly assigned 1905 patients with left main coronary artery disease of low or intermediate anatomical complexity (according to assessment at the participating centers) to undergo either PCI with fluoropolymer-based cobalt–chromium everolimus-eluting stents (PCI group, 948 patients) or CABG (CABG group, 957 patients). The primary outcome was a composite of death, stroke, or myocardial infarction.

RESULTS

At 5 years, a primary outcome event had occurred in 22.0% of the patients in the PCI group and in 19.2% of the patients in the CABG group (difference, 2.8 percentage points; 95% confidence interval [CI], −0.9 to 6.5; P=0.13). Death from any cause occurred more frequently in the PCI group than in the CABG group (in 13.0% vs. 9.9%; difference, 3.1 percentage points; 95% CI, 0.2 to 6.1). In the PCI and CABG groups, the incidences of definite cardiovascular death (5.0% and 4.5%, respectively; difference, 0.5 percentage points; 95% CI, −1.4 to 2.5) and myocardial infarction (10.6% and 9.1%; difference, 1.4 percentage points; 95% CI, −1.3 to 4.2) were not significantly different. All cerebrovascular events were less frequent after PCI than after CABG (3.3% vs. 5.2%; difference, −1.9 percentage points; 95% CI, −3.8 to 0), although the incidence of stroke was not significantly different between the two groups (2.9% and 3.7%; difference, −0.8 percentage points; 95% CI, −2.4 to 0.9). Ischemia-driven revascularization was more frequent after PCI than after CABG (16.9% vs. 10.0%; difference, 6.9 percentage points; 95% CI, 3.7 to 10.0).

CONCLUSIONS

In patients with left main coronary artery disease of low or intermediate anatomical complexity, there was no significant difference between PCI and CABG with respect to the rate of the composite outcome of death, stroke, or myocardial infarction at 5 years. (Funded by Abbott Vascular; EXCEL ClinicalTrials.gov number, NCT01205776. opens in new tab.)

https://www.nejm.org/doi/full/10.1056/NEJMoa1909406

 

Is the Tide Turning on the ‘Grubby’ Affair of EXCEL and the European Guidelines?

Taggart was chair of the surgical committee for the Abbott-sponsored EXCEL trial, which compared two procedures for patients who had blockages in their left main coronary artery: percutaneous coronary intervention (PCI) using coronary stents, and coronary artery bypass graft surgery (CABG). The investigators designed the trial to compare outcomes for the two treatments using a composite endpoint of death, stroke, and myocardial infarction (MI). The 3-year follow-up data had been published in NEJM without controversy — or, at least, without public controversy.

But when it came time to publish the 5-year follow-up, there was a significantly higher rate of death in the stent group, and both Taggart and the journal editors were concerned that this finding was being downplayed in the manuscript.

In their comments to the authors, the journal editors had recommended including the mortality difference (unless clearly trivial) ‘”in the concluding statement in the final paragraph.” Yet, the concluding statement of the published paper read that there “was no significant difference between PCI and CABG.”

Over a year after the BBC received the leaked data, the EXCEL investigators published an analysis of the primary outcome using the universal definition of MI data in the Journal of the American College of Cardiology.

It shows 141 events in the PCI arm compared to 102 in the CABG arm. The investigators acknowledge that the rates of procedural MI differ depending on the definition used. According to their analysis, the protocol definition was predictive of mortality after both treatments, whereas the universal definition of procedural MI was predictive of mortality only after CABG. Not everyone agrees with this interpretation, and an accompanying editorial questioned these conclusions.

As for the guidelines, the tide may be turning.

In a joint statement with EACTS on October 6, 2020, the ESC agreed to review its guidelines for left main disease in the light of emerging, longer-term outcome data from the trials of CABG vs PCI.

SOURCE

https://www.medscape.com/viewarticle/939944?src=WNL_infoc_201226_MSCPEDIT_excel2&uac=93761AJ&impID=2758606&faf=1#vp_5

UPDATED on 9/4/2019

SYNTAX at 10 Years: Bypass vs PCI Still a Toss-Up Overall

But CABG beats stenting for important subgroups

SOURCE

https://www.medpagetoday.com/meetingcoverage/esc/81944?xid=nl_mpt_DHE_2019-09-04&eun=g99985d0r&utm_source=Sailthru&utm_medium=email&utm_campaign=Daily%20Headlines%202019-09-04&utm_term=NL_Daily_DHE_Active

Lancet Study, 2/2018

Interpretation

CABG had a mortality benefit over PCI in patients with multivessel disease, particularly those with diabetes and higher coronary complexity. No benefit for CABG over PCI was seen in patients with left main disease. Longer follow-up is needed to better define mortality differences between the revascularisation strategies.

JACC Study, 7/2018

CONCLUSIONS

This individual patient-data pooled analysis demonstrates that 5-year stroke rates are significantly lower after PCI compared with CABG, driven by a reduced risk of stroke in the 30-day post-procedural period but a similar risk of stroke between 31 days and 5 years. The greater risk of stroke after CABG compared with PCI was confined to patients with multivessel disease and diabetes. Five-year mortality was markedly higher for patients experiencing a stroke within 30 days after revascularization.

European Journal of Cardiothoracic Surgery Study, 6/2018

CONCLUSIONS

Despite a longer length of hospital stay, patients with impaired LVF requiring intervention for coronary artery disease experienced a greater post-procedural survival benefit if they received CABG compared to PCI. We have demonstrated this at 30 days, 90 days, 1 year, 3 years, 5 years and 8 years following revascularization. At present, CABG remains a superior revascularization modality to PCI in patients with poor LVF.

 

New Studies on Clinical Outcomes from two Revascularization Strategies: CABG and PCI

 

J Am Coll Cardiol. 2018 Jul 24;72(4):386-398. doi: 10.1016/j.jacc.2018.04.071.

Stroke Rates Following Surgical Versus Percutaneous Coronary Revascularization.

Abstract

BACKGROUND:

Coronary artery bypass grafting (CABG) and percutaneous coronary intervention (PCI) are used for coronary revascularization in patients with multivessel and left main coronary artery disease. Stroke is among the most feared complications of revascularization. Due to its infrequency, studies with large numbers of patients are required to detect differences in stroke rates between CABG and PCI.

OBJECTIVES:

This study sought to compare rates of stroke after CABG and PCI and the impact of procedural stroke on long-term mortality.

METHODS:

We performed a collaborative individual patient-data pooled analysis of 11 randomized clinical trials comparing CABG with PCI using stents; ERACI II (Argentine Randomized Study: Coronary Angioplasty With Stenting Versus Coronary Bypass Surgery in Patients With Multiple Vessel Disease) (n = 450), ARTS (Arterial Revascularization Therapy Study) (n = 1,205), MASS II (Medicine, Angioplasty, or Surgery Study) (n = 408), SoS (Stent or Surgery) trial (n = 988), SYNTAX (Synergy Between Percutaneous Coronary Intervention With Taxus and Cardiac Surgery) trial (n = 1,800), PRECOMBAT (Bypass Surgery Versus Angioplasty Using Sirolimus-Eluting Stent in Patients With Left Main Coronary Artery Disease) trial (n = 600), FREEDOM (Comparison of Two Treatments for Multivessel Coronary Artery Disease in Individuals With Diabetes) trial (n = 1,900), VA CARDS (Coronary Artery Revascularization in Diabetes) (n = 198), BEST (Bypass Surgery Versus Everolimus-Eluting Stent Implantation for Multivessel Coronary Artery Disease) (n = 880), NOBLE (Percutaneous Coronary Angioplasty Versus Coronary Artery Bypass Grafting in Treatment of Unprotected Left Main Stenosis) trial (n = 1,184), and EXCEL (Evaluation of Xience Versus Coronary Artery Bypass Surgery for Effectiveness of Left Main Revascularization) trial (n = 1,905). The 30-day and 5-year stroke rates were compared between CABG and PCI using a random effects Cox proportional hazards model, stratified by trial. The impact of stroke on 5-year mortality was explored.

RESULTS:

The analysis included 11,518 patients randomly assigned to PCI (n = 5,753) or CABG (n = 5,765) with a mean follow-up of 3.8 ± 1.4 years during which a total of 293 strokes occurred. At 30 days, the rate of stroke was 0.4% after PCI and 1.1% after CABG (hazard ratio [HR]: 0.33; 95% confidence interval [CI]: 0.20 to 0.53; p < 0.001). At 5-year follow-up, stroke remained significantly lower after PCI than after CABG (2.6% vs. 3.2%; HR: 0.77; 95% CI: 0.61 to 0.97; p = 0.027). Rates of stroke between 31 days and 5 years were comparable: 2.2% after PCI versus 2.1% after CABG (HR: 1.05; 95% CI: 0.80 to 1.38; p = 0.72). No significant interactions between treatment and baseline clinical or angiographic variables for the 5-year rate of stroke were present, except for diabetic patients (PCI: 2.6% vs. CABG: 4.9%) and nondiabetic patients (PCI: 2.6% vs. CABG: 2.4%) (p for interaction = 0.004). Patients who experienced a stroke within 30 days of the procedure had significantly higher 5-year mortality versus those without a stroke, both after PCI (45.7% vs. 11.1%, p < 0.001) and CABG (41.5% vs. 8.9%, p < 0.001).

CONCLUSIONS:

This individual patient-data pooled analysis demonstrates that 5-year stroke rates are significantly lower after PCI compared with CABG, driven by a reduced risk of stroke in the 30-day post-procedural period but a similar risk of stroke between 31 days and 5 years. The greater risk of stroke after CABG compared with PCI was confined to patients with multivessel disease and diabetes. Five-year mortality was markedly higher for patients experiencing a stroke within 30 days after revascularization.

KEYWORDS:

coronary artery bypass graft; left main; mortality; multivessel; percutaneous coronary intervention; stenting; stroke

PMID:
30025574
DOI:
10.1016/j.jacc.2018.04.071

 

Lancet Study

Head SJ, Milojevic M, Daemen J, Ahn JM, Boersma E, Christiansen EH, Domanski MJ, Farkouh ME, Flather M, Fuster V, Hlatky MA, Holm NR, Hueb WA, Kamalesh M, Kim YH, Mäkikallio T, Mohr FW, Papageorgiou G, Park SJ, Rodriguez AE, Sabik JF, Stables RH, Stone GW, Serruys PW, Kappetein AP. Mortality after coronary artery bypass grafting versus percutaneous coronary intervention with stenting for coronary artery disease: a pooled analysis of individual patient data. Lancet. 2018 Feb 22 [Epub ahead of print]. doi: 10.1016/S0140-6736(18)30423-9. PMID: 29478841

Summary

Background

Numerous randomised trials have compared coronary artery bypass grafting (CABG) with percutaneous coronary intervention (PCI) for patients with coronary artery disease. However, no studies have been powered to detect a difference in mortality between the revascularisation strategies.

Methods

We did a systematic review up to July 19, 2017, to identify randomised clinical trials comparing CABG with PCI using stents. Eligible studies included patients with multivessel or left main coronary artery disease who did not present with acute myocardial infarction, did PCI with stents (bare-metal or drug-eluting), and had more than 1 year of follow-up for all-cause mortality. In a collaborative, pooled analysis of individual patient data from the identified trials, we estimated all-cause mortality up to 5 years using Kaplan-Meier analyses and compared PCI with CABG using a random-effects Cox proportional-hazards model stratified by trial. Consistency of treatment effect was explored in subgroup analyses, with subgroups defined according to baseline clinical and anatomical characteristics.

Findings

We included 11 randomised trials involving 11 518 patients selected by heart teams who were assigned to PCI (n=5753) or to CABG (n=5765). 976 patients died over a mean follow-up of 3·8 years (SD 1·4). Mean Synergy between PCI with Taxus and Cardiac Surgery (SYNTAX) score was 26·0 (SD 9·5), with 1798 (22·1%) of 8138 patients having a SYNTAX score of 33 or higher. 5 year all-cause mortality was 11·2% after PCI and 9·2% after CABG (hazard ratio [HR] 1·20, 95% CI 1·06–1·37; p=0·0038). 5 year all-cause mortality was significantly different between the interventions in patients with multivessel disease (11·5% after PCI vs 8·9% after CABG; HR 1·28, 95% CI 1·09–1·49; p=0·0019), including in those with diabetes (15·5% vs 10·0%; 1·48, 1·19–1·84; p=0·0004), but not in those without diabetes (8·7% vs 8·0%; 1·08, 0·86–1·36; p=0·49). SYNTAX score had a significant effect on the difference between the interventions in multivessel disease. 5 year all-cause mortality was similar between the interventions in patients with left main disease (10·7% after PCI vs 10·5% after CABG; 1·07, 0·87–1·33; p=0·52), regardless of diabetes status and SYNTAX score.

Interpretation

CABG had a mortality benefit over PCI in patients with multivessel disease, particularly those with diabetes and higher coronary complexity. No benefit for CABG over PCI was seen in patients with left main disease. Longer follow-up is needed to better define mortality differences between the revascularisation strategies.

SOURCE

European Journal of Cardiothoracic Surgery Study, 6/2018

 

Eur J Cardiothorac Surg. 2018 Jun 22. doi: 10.1093/ejcts/ezy236. [Epub ahead of print]

Comparison of the survival between coronary artery bypass graft surgery versus percutaneous coronary intervention in patients with poor left ventricular function (ejection fraction <30%): a propensity-matched analysis.

Abstract

OBJECTIVES:

Existing evidence comparing the outcomes of coronary artery bypass graft (CABG) surgery versus percutaneous coronary intervention (PCI) in patients with poor left ventricular function (LVF) is sparse and flawed. This is largely due to patients with poor LVF being underrepresented in major research trials and the outdated nature of some studies that do not consider drug-eluting stent PCI.

METHODS:

Following strict inclusion criteria, 717 patients who underwent revascularization by CABG or PCI between 2002 and 2015 were enrolled. All patients had poor LVF (defined by ejection fraction <30%). By employing a propensity score analysis, 134 suitable matches (67 CABG and 67 PCI) were identified. Several outcomes were evaluated, in the matched population, using data extracted from national registry databases.

RESULTS:

CABG patients required a longer length of hospital stay post-revascularization compared to PCI in the propensity-matched population, 7 days (lower-upper quartile; 6-12) and 2 days (lower-upper quartile; 1-6), respectively (Mood’s median test, P = 0.001). Stratified Cox-regression proportional-hazards analysis of the propensity-matched population found that PCI patients experienced a higher adjusted 8-year mortality rate (hazard ratio 3.291, 95% confidence interval 1.776-6.101; P < 0.001). This trend was consistent amongst urgent cases of revascularization: patients with 3 or more vessels with coronary artery disease and patients where complete revascularization was achieved. Although sub-analyses found no difference between survival distributions of on-pump versus off-pump CABG (log-rank P = 0.726), both modes of CABG were superior to PCI (stratified log-rank P = 0.002).

CONCLUSIONS:

Despite a longer length of hospital stay, patients with impaired LVF requiring intervention for coronary artery disease experienced a greater post-procedural survival benefit if they received CABG compared to PCI. We have demonstrated this at 30 days, 90 days, 1 year, 3 years, 5 years and 8 years following revascularization. At present, CABG remains a superior revascularization modality to PCI in patients with poor LVF.

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