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Accelerating PROTAC drug discovery: Establishing a relationship between ubiquitination and target protein degradation

Curator: Stephen J. Williams, Ph.D.

PROTACs have been explored in multiple disease fields with focus on only few ligases like cereblon (CRBN), Von Hippel-Lindau (VHL), IAP and MDM2. Cancer targets like androgen receptor, estrogen receptor, BTK, BCL2, CDK8 and c-MET [[6], [7], [8], [9], [10], [11]] have been successfully targeted using PROTACs. A variety of BET family (BRD2, BRD3, and BRD4)- PROTACs were designed using multiple ligases; MDM2-based BRD4 PROTAC [12], CRBN based dBET1 [13] and BETd-24-6 [14] for triple-negative breast cancer, enhanced membrane permeable dBET6 [15], and dBET57 PROTAC [16]. PROTACs for Hepatitis c virus (HCV) protease, IRAK4 and Tau [[17], [18], [19]] have been explored for viral, immune and neurodegenerative diseases, respectively. Currently, the PROTAC field expansion to vast undruggable proteome is hindered due to narrow focus on select E3 ligases. Lack of reliable tools to rapidly evaluate PROTACs based on new ligases is hindering the progress. Screening platforms designed must be physiologically relevant and represent true PROTAC cellular function, i.e., PROTAC-mediated target ubiquitination and degradation.

In the current study, we employ TUBEs as affinity capture reagents to monitor PROTAC-induced poly-ubiquitination and degradation as a measure of potency. We established and validated proof-of-concept cell-based assays in a 96-well format using PROTACS for three therapeutic targets BET family proteins, kinases, and KRAS. To our knowledge, the proposed PROTAC assays are first of its kind that can simultaneously 1) detect ubiquitination of endogenous, native protein targets, 2) evaluate the potency of PROTACs, and 3) establish a link between the UPS and protein degradation. Using these TUBE assays, we established rank order potencies between four BET family PROTACs dBET1, dBET6, BETd246 and dBET57 based on peak ubiquitination signals (“UbMax”) of the target protein. TUBE assay was successful in demonstrating promiscuous kinase PROTACs efficiency to degrade Aurora Kinase A at sub-nanomolar concentrations within 1 h. A comparative study to identify changes in the ubiquitination and degradation profile of KRAS G12C PROTACs recruiting two E3 ligases (CRBN and VHL). All of the ubiquitination and degradation profiles obtained from TUBE based assays correlate well with traditional low throughput immunoblotting. Significant correlation between DC50 obtained from protein degradation in western blotting and UbMax values demonstrates our proposed assays can aid in high-throughput screening and drastically eliminate artifacts to overcome bottlenecks in PROTAC drug discovery.

To successfully set up HTS screening with novel PROTACs without pre-existing knowledge, we recommend the following steps. 1. Identify a model PROTAC that can potentially demonstrate activity based on knowledge in PROTAC design or in vitro binding studies. 2. Perform a time course study with 2–3 doses of the model PROTAC based on affinities of the ligands selected. 3. Monitor ubiquitination and degradation profiles using plate-based assay and identify time point that demonstrates UbMax. 4. Perform a dose response at selected time point with a library of PROTACs to establish rank order potency.

INTRODUCTION

Ubiquitination is a major regulatory mechanism to maintain cellular protein homeostasis by marking proteins for proteasomal-mediated degradation [1]. Given ubiquitin’s role in a variety of pathologies, the idea of targeting the Ubiquitin Proteasome System (UPS) is at the forefront of drug discovery [2]. “Event-driven” protein degradation using the cell’s own UPS is a promising technology for addressing the “undruggable” proteome [3]. Targeted protein degradation (TPD) has emerged as a new paradigm and promising therapeutic option to selectively attack previously intractable drug targets using PROteolytic TArgeting Chimeras (PROTACs) [4]. PROTACs are heterobifunctional molecules with a distinct ligand that targets a specific E3 ligase which is tethered to another ligand specific for the target protein using an optimized chemical linker. A functional PROTAC induces a ternary E3-PROTAC-target complex, resulting in poly-ubiquitination and subsequent controlled protein degradation [5]. Ability to function at sub-stoichiometric levels for efficient degradation, a significant advantage over traditional small molecules.

PROTACs have been explored in multiple disease fields with focus on only few ligases like cereblon (CRBN), Von Hippel-Lindau (VHL), IAP and MDM2. Cancer targets like androgen receptorestrogen receptor, BTK, BCL2, CDK8 and c-MET [[6][7][8][9][10][11]] have been successfully targeted using PROTACs. A variety of BET family (BRD2, BRD3, and BRD4)- PROTACs were designed using multiple ligases; MDM2-based BRD4 PROTAC [12], CRBN based dBET1 [13] and BETd-24-6 [14] for triple-negative breast cancer, enhanced membrane permeable dBET6 [15], and dBET57 PROTAC [16]. PROTACs for Hepatitis c virus (HCV) proteaseIRAK4 and Tau [[17][18][19]] have been explored for viral, immune and neurodegenerative diseases, respectively. Currently, the PROTAC field expansion to vast undruggable proteome is hindered due to narrow focus on select E3 ligases. Lack of reliable tools to rapidly evaluate PROTACs based on new ligases is hindering the progress. Screening platforms designed must be physiologically relevant and represent true PROTAC cellular function, i.e., PROTAC-mediated target ubiquitination and degradation.

Cellular PROTAC screening is traditionally performed using cell lines harboring reporter genes and/or Western blotting. While Western blotting is easy to perform, they are low throughput, semi-quantitative and lack sensitivity. While reporter gene assays address some of the issues, they are challenged by reporter tags having internal lysines leading to artifacts. Currently, no approaches are available that can identify true PROTAC effects such as target ubiquitination and proteasome-mediated degradation simultaneously. High affinity ubiquitin capture reagents like TUBEs [20] (tandem ubiquitin binding entities), are engineered ubiquitin binding domains (UBDs) that allow for detection of ultralow levels of polyubiquitinated proteins under native conditions with affinities as low as 1 nM. The versatility and selectivity of TUBEs makes them superior to antibodies, and they also offer chain-selectivity (-K48, -K63, or linear) [21]. High throughput assays that can report the efficacy of multiple PROTACs simultaneously by monitoring PROTAC mediated ubiquitination can help establish rank order potency and guide chemists in developing meaningful structure activity relationships (SAR) rapidly.

In the current study, we employ TUBEs as affinity capture reagents to monitor PROTAC-induced poly-ubiquitination and degradation as a measure of potency. We established and validated proof-of-concept cell-based assays in a 96-well format using PROTACS for three therapeutic targets BET family proteins, kinases, and KRAS. To our knowledge, the proposed PROTAC assays are first of its kind that can simultaneously 1) detect ubiquitination of endogenous, native protein targets, 2) evaluate the potency of PROTACs, and 3) establish a link between the UPS and protein degradation. Using these TUBE assays, we established rank order potencies between four BET family PROTACs dBET1, dBET6, BETd246 and dBET57 based on peak ubiquitination signals (“UbMax”) of the target protein. TUBE assay was successful in demonstrating promiscuous kinase PROTACs efficiency to degrade Aurora Kinase A at sub-nanomolar concentrations within 1 h. A comparative study to identify changes in the ubiquitination and degradation profile of KRAS G12C PROTACs recruiting two E3 ligases (CRBN and VHL). All of the ubiquitination and degradation profiles obtained from TUBE based assays correlate well with traditional low throughput immunoblotting. Significant correlation between DC50 obtained from protein degradation in western blotting and UbMax values demonstrates our proposed assays can aid in high-throughput screening and drastically eliminate artifacts to overcome bottlenecks in PROTAC drug discovery.

Fig. 1. Schematic representation of TUBE assay to monitor PROTAC mediated cellular ubiquitination of target proteins.
Fig. 2. TUBE based assay screening of PROTACs: Jurkat cell lysates were treated with BRD3-specific PROTACs A) dBET1, B) dBET6, C) BETd24-6, and D) dBET57. Polyubiquitination profiles and Ubmax of BRD3 for each PROTAC were represented as relative CL intensity. Relative CL intensities were calculated by dividing raw CL signals from a given PROTAC dose over DMSO treated samples. Error bars represent standard deviations, n = 3.
Fig. 3. PROTAC mediated degradation of bromodomain proteins analyzed by anti-BRD3 western blotting. Dose response of PROTACs dBET1, dBET6, Betd-24-6 and dBET57 at 45 min in Jurkat cells demonstrates degradation of BRD3, Acting as loading control.

 

 

 

 

 

 

 

 

 

Fig. 4. PROTAC mediated ubiquitination and degradation of AURKA in K562 cells. (A) Time course study to evaluate intracellular ubiquitination and degradation. (B) Western blot analysis of time course study: degradation kinetics (C) A dose response study to evaluate DC50 of the promiscuous kinase PROTAC in K562 cells. (D) Western blot analysis of dose response study to monitor degradation, GAPDH as loading control. Error bars represent standard deviation, n = 3.

SOURCE

https://www.sciencedirect.com/science/article/abs/pii/S0006291X22011792

Other articles of PROTACs in this Open Access Journal Include

The Vibrant Philly Biotech Scene: Proteovant Therapeutics Using Artificial Intelligence and Machine Learning to Develop PROTACs

The Map of human proteins drawn by artificial intelligence and PROTAC (proteolysis targeting chimeras) Technology for Drug Discovery

Live Conference Coverage AACR 2020 in Real Time: Monday June 22, 2020 Late Day Sessions

From High-Throughput Assay to Systems Biology: New Tools for Drug Discovery

 

2022 Albert Lasker Basic Medical Research Award for Integrins—Mediators of Cell-Matrix and Cell-Cell Adhesion

Reporter: Aviva Lev-Ari, PhD, RN

 

The three recipients of 2022 Albert Lasker Basic Medical Research Award For discoveries concerning the integrins—key mediators of cell-matrix and cell-cell adhesion in physiology and disease are:

  • Richard O. Hynes, Massachusetts Institute of Technology
  • Erkki Ruoslahti, Sanford Burnham Prebys
  • Timothy A. Springer, Boston Children’s Hospital/Harvard Medical School

2022 Basic Award video

https://www.youtube.com/watch?v=4k60P3Pnh30

Acceptance remarks

Watch 3 Videos
 
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Figure 1A: Pairs that bond
Two protein chains, α and ß, compose the heterodimeric integrins that span the cell membrane. The portion outside affixes to molecules in the extracellular matrix (ECM) or on other cells. Adherence through integrins triggers cytoskeleton assembly and vice versa. Such events can also influence the behavior of other proteins inside the cell. The image shows the matrix-cell type of integrin; a second type mediates cell-cell interactions.
Illustration: Cassio Lynm / © Amino Creative

Figure 1B: Families that stick together
Integrin α and ß subunit each belong to a family of proteins with a shared evolutionary ancestor. Individual members of the α and ß families combine in different ways to create 24 mammalian heterodimers that physically associate with a variety of molecules. In the ECM, these binding partners include collagen, laminin, and other RGD-containing proteins such as fibronectin and fibrinogen; on cells, these partners include proteins such as ICAM-1, which dwells on the surface of white blood cells and cells that line blood vessels. The first integrin identified, the platelet receptor, promotes blood clotting. LFA-1 helps immune cells fight infections in numerous ways.
Illustration: Cassio Lynm / © Amino Creative

Figure 2: Fleeting attachments, profound effects
By fostering adherence between cells and the ECM or other cells, integrins play a key role in a tremendous number of essential physiological interactions.
Illustration: Cassio Lynm / © Amino Creative

Figures Source: 

https://laskerfoundation.org/winners/integrins-mediators-of-cell-matrix-cell-adhesion/

 

Selected Publications – Discovery of Integrins

Cell-Matrix Interactions

Ruoslahti, E., Vaheri. A., Kuusela, P., and Linder, E. (1973). Fibroblast surface antigen: a new serum protein. Biochim. BiophysActa. 322, 352-358.

Hynes, R.O. (1973). Alteration of cell-surface proteins by viral transformation and by proteolysis. Proc. Natl. Acad. Sci. USA70, 3170-3174.

Pierschbacher, M.D., and Ruoslahti, E. (1984). Cell attachment activity of fibronectin can be duplicated by small synthetic fragments of the molecule. Nature309, 30-33.

Pytela, R., Pierschbacher, M.D., and Ruoslahti, E. (1985). A 125/115-kDa cell surface receptor specific for vitronectin interacts with the arginine-glycine-aspartic acid adhesion sequence derived from fibronectin. Proc. Natl. Acad. Sci. USA. 82, 5766-5770.

Pytela, R., Pierschbacher, M.D., Ginsberg, M.H., Plow, E.F., and Ruoslahti, E. (1986). Platelet membrane glycoprotein IIb/IIIa: member of a family of Arg-Gly-Asp-specific adhesion receptors. Science231, 1559-1562.

Tamkun, J.W., DeSimone, D.W., Fonda, D., Patel, R.S., Buck, C., Horwitz, A.F., and Hynes, R.O. (1986). Structure of integrin, a glycoprotein involved in the transmembrane linkage between fibronectin and actin. Cell. 46, 271-282.

Hynes, R.O. (1987). Integrins: a family of cell surface receptors. Cell48, 549-554.

Ruoslahti, E. (1996). RGD and other recognition sequences for integrins. Annu. Rev. Cell Dev. Biol. 12, 697-715.

Hynes, R.O. (2002). Integrins: bidirectional allosteric signaling machines. Cell. 110, 673-687.

Cell-Cell Interactions

Kurzinger, K., Reynolds, T., Germain, R.N., Davignon, D., Martz, E., and Springer, T.A. (1981). A novel lymphocyte function-associated antigen (LFA-1): cellular distribution, quantitative expression, and structure. J. Immunol. 127, 596-600.

Sanchez-Madrid, F., Nagy, J., Robbins, E., Simon, P., and Springer, T.A. (1983). A human leukocyte differentiation antigen family with distinct alpha subunits and a common beta subunit: the lymphocyte function-associated antigen (LFA-1), the C3bi complement receptor (OKM1/Mac-1), and the p150,95 molecule. J. Exp. Med. 158, 1785-1789.

Thompson, W.S., Miller, L.J., Schmalstieg, F.C., Anderson, D.C., and Springer, T.A. (1984). Inherited deficiency of the Mac-1, LFA-1, p150,95 glycoprotein family and its molecular basis. J. Exp. Med. 160, 1901-1905.

Kishimoto, T.K., Lee, A., Roberts, T.M., and Springer, T.A. (1987). Cloning of the beta subunit of the leukocyte adhesion proteins: homology to an extra-cellular matrix receptor defines a novel supergene family. Cell. 48, 681-690.

Makgoba. M.W., Sanders, M.E., Luce, G.E.G., Dustin, M.L., Springer, T.A., Clark, E.A., Mannoni, P., and Shaw, S. (1988). ICAM-1 a ligand for LFA-1-dependent adhesion of B, T and myeloid cells. Nature331, 86-88.

Staunton, D.E., Dustin, M.L., and Springer, T.A. (1989). Functional cloning of ICAM-2, a cell adhesion ligand for LFA-1 homologous to ICAM-1. Nature. 339, 61-65.

Springer, T.A. (1990). Adhesion receptors of the immune system. Nature. 346, 425-434.

Lawrence, M.B., and Springer, T.A. (1991). Leukocytes roll on a selectin at physiologic flow rates: distinction from and prerequisite for adhesion through integrins. Cell. 65, 859-873.

Luo, B.-H., Carman, C.V., and Springer, T.A. (2007) Structural basis of integrin regulation and signaling. Annu. Rev. Immunol. 25, 619-647.

Li, J., Yan, J., and Springer, T.A. (2021). Low-affinity integrin states have faster ligand-binding kinetics than the high-affinity state. eLife. 10, 1-22. e73359. doi: 10.7554/eLife.73359.

SOURCE

Clarivate Analytics – a Powerhouse in IP assets and in Pharmaceuticals Informercials

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

We addressed in the past in several articles the emergence of Clarivate in its new life post Reuters years which ended by a SPAC IPO in 2019. This articles included:

  • Clarivate Analytics expanded IP data leadership by new acquisition of the leading provider of intellectual property case law and analytics Darts-ip

https://pharmaceuticalintelligence.com/2019/12/02/clarivate-analytics-expanded-ip-data-leadership-by-new-acquisition-of-the-leading-provider-of-intellectual-property-case-law-and-analytics-darts-ip/

  • Innovation and Patent Activity during COVID-19 from Clarivate – Survey Results Published

https://pharmaceuticalintelligence.com/2020/06/30/innovation-and-patent-activity-during-covid-19-from-clarivate-survey-result-published/

  • Chasing change: Innovation and patent activity during COVID-19

https://pharmaceuticalintelligence.com/2020/07/02/chasing-change-innovation-and-patent-activity-during-covid-19/

  • Potential Use of LPBI IP as Value Price Driver by Potential Acquirer: Assumptions per Asset Class

 https://pharmaceuticalintelligence.com/2019-vista/potential-use-of-lpbi-ip-as-value-price-driver-by-potential-acquirer-assumptions-per-asset-class/

  • AI Acquisitions by Big Tech Firms Are Happening at a Blistering Pace: 2019 Recent Data by CBI Insights

https://pharmaceuticalintelligence.com/2019/12/11/ai-acquisitions-by-big-tech-firms-are-happening-at-a-blistering-pace-2019-recent-data-by-cbiinsights/

  • WHAT ARE LPBI Group’s NEEDS in June 2019 – Aviva’s BOLD VISION on June 11, 2019

https://pharmaceuticalintelligence.com/2019-vista/what-are-lpbi-groups-needs-in-june-2019-avivas-bold-vision-on-june-11-2019/

  • Opportunities Map for LPBI Group’s three Intellectual Property Asset Classes of Digital Published Products in the Acquisition Arena

https://pharmaceuticalintelligence.com/2019-vista/opportunities-map-in-the-acquisition-arena/

  • Multiple Major Scientific Journals Will Fully Adopt Open Access Under Plan S

https://pharmaceuticalintelligence.com/2020/09/10/multiple-major-scientific-journals-will-fully-adopt-open-access-under-plan-s/

 

In this curation I wish to showcase Clarivate as a result of a successful SPAC as presented in Financial Times article

The Spac sponsor bonanza

 

https://www.ft.com/content/9b481c63-f9b4-4226-a639-238f9fae4dfc

Few have replicated Mr Klein’s success, which he achieved after using a Spac to take the data company Clarivate Analytics public in 2019

Please use the sharing tools found via the share button at the top or side of articles. Copying articles to share with others is a breach of FT.com T&Cs and Copyright Policy. Email licensing@ft.com to buy additional rights. Subscribers may share up to 10 or 20 articles per month using the gift article service. More information can be found here.
https://www.ft.com/content/9b481c63-f9b4-4226-a639-238f9fae4dfc

That moment in June in which Mr Klein and his partners cashed in more than $60m came after the stock had doubled to more than $20, in part thanks to a deal to buy the intellectual property management and technology company CPA Global. Onex and Barings, the two private equity firms that owned Clarivate before it went public via Mr Klein’s Spac, also sold stock at the same time.

Please use the sharing tools found via the share button at the top or side of articles. Copying articles to share with others is a breach of FT.com T&Cs and Copyright Policy. Email licensing@ft.com to buy additional rights. Subscribers may share up to 10 or 20 articles per month using the gift article service. More information can be found here.
https://www.ft.com/content/9b481c63-f9b4-4226-a639-238f9fae4dfc

Clarivate’s share price has since risen to $27.69, so the value of Mr Klein’s remaining stake has continued to swell and his investor group still holds shares worth $395m. The group also has separate warrants on top further augmenting their potential profit.

See Figure 

SPAC IPO, 11/2018, $10/share

–>>> Merger, 3/2019, $10/share

–>>>Clarivate PLC, 11/2020, $27/share

… asymmetry of Spac mathematics: the risk in Spacs falls most heavily on outside shareholders even as the return on investment for sponsors looks very promising indeed.

SOURCE

https://www.ft.com/content/9b481c63-f9b4-4226-a639-238f9fae4dfc

 

It worth exploring the synergies embedded in a potential acquisition of LPBI Groups Portfolio of IP Assets by Clarivate Analytics, a publishing company that has the infrastructure needed for promotion of LPBI Group’s content in Pharmaceutical Media, Medicine, Life Sciences and Health care and for Monetization of this content.

Portfolio of IP Assets

 

Near Term Investment Outlook for 2023: A Perspective from Advisors Potentially Affecting M&A Landscape

Curator: Stephen J. Williams, Ph.D.

The following is an adaptation from various reports and the forseen changes in forecast for different sectors as well as the general investment landscape for the near future (2022-2023). Of course projections may change given changes in undewrlying fundamentals.

Many financial advisors and professionals feel the U.S. is in a late-cycle for its economy, with a significant slowing of corporate earnings in the midst of higher than usual inflation {although inflation estimates are being halved from its current 8-10% for next year}.    Consensus investment strategies deemed favorable include US (not international) equities with high quality assest and away from cyclicals.  This represents the near end of a business cycle.  As growth returns and interest rates increase we may seen the entrance into a new business cycle, although this may not happen until later 2023.  In general, it is advised investors move out of cyclicals as the economy continues to slow and into large and mid cap US equities.

This change in landscape may be very favorable to the overall Health Care and Information Technology sectors.  In health care, Life Sciences Tools and Services as well as Medical Devices are expected to outperform.  In IT, IT Services, software and Networking are favored sectors while communication services like Publishing Services are considered to be Neutral to Unfavorable.

What does this mean for Life Sciences and Health Related small companies looking for an Exit or M&A strategies?

With higher interest rates, credit markets may continue to deteriote and companies may have to look toward Global Macro to find any funding through cash or credit markets.  Equity Hedge strategies may be neutral to unfavorable with Event Driven opportunities like distressed deals  unfavorable but most analysts do consider Merger Arbitrage as Event Driven strategy to be favorable.  A competitive and narrow merger and acquisition environment is expected to last through 2023.

A general consensus for a neutroal environment is seen for most Private Equity, although a more favorable environment for small and mid cap buyouts may exist.  Recent short term weakness in the IT sector has led to diminished exit valuations however this may be a good entry point for Growth Equity and Venture Capital.  Private Debt strategies look unfavorable due to potential US recessions and potential underwriting issues.  Therefore Favored Private Capital strategies include Private Equity for Small and Mid Cap Buyouts and Growth Equity and Venture Capital.

Sources:

https://www.wellsfargo.com/investment-institute/2022-midyear-outlook/

Deals to pick up in second half of 2022

All of the stars are aligned for there to be a flurry of deals activity across all areas of the sector despite the slow start to the year so far. Many large pharma players are flush with cash (particularly those that have COVID-19 treatments in their arsenal), biotech valuations have been normalizing after years of a boom market and the 2025 patent cliff is rapidly approaching, all making for a strong deal environment.

Given the broader labor changes, supply shortages and constantly changing supply chain strategies and operations, the focus on quality can be challenging to sustain. Yet the downside can have massive impacts on businesses, including the potential inability to manufacture products.

The long litany of macroeconomic and regulatory headwinds has CEOs looking for transactions that are easily integrated and will get cash off their balance sheet as inflationary pressures mount. 


Pharmaceutical & life sciences deals outlook

Increased scrutiny from the US Federal Trade Commission (FTC) around larger deals could mean that 2022 will be a year of bolt-on transactions in the $5 to $15 billion range as pharma companies take multiple shots on goal in order to make up for revenues lost to generic competition in the remainder of the decade. However, don’t rule out the potential for larger deals ⁠— consolidation is good for the health ecosystem and drives broader efficiency.

Expect to see big pharma picking up earlier stage companies to try and fill the pipeline gaps that are likely to start in 2024. While market conditions suggest bargain prices for biotech are possible, recent transactions indicate that pharma companies are still paying significantly above current trading prices (ranging from approximately 50 to 100% of current trading), but below the peak valuations of recent memory.

In the first few months of the year, semi-annualized deal value was down 58% from the same period last year, with companies investing just $61.7 billion so far. Only 137 deals were announced during that time, compared to 204 in the year-prior period.

Talk of drug pricing regulations continues in Washington as Congress bats around a pared down version of the Build Back Better plan. Expect some of that tension to ease in the fall if a new Congress takes on a different agenda.

Other areas of the sector like medical devices face similar headwinds from regulators, and continue to deal with a greater impact from semiconductor shortages. Even though semi-annualized deal value in the medical device space is down 85% from the same period the prior year, expect these companies to remain focused on M&A as the subsector searches for alternative forms of revenue ⁠— particularly from new consumer-centric technologies.

Macroeconomic headwinds and geopolitical tensions have created volatility in spending at CDMOs and CROs, limiting their willingness to deploy capital as the uncertainty persists. 

Source: https://www.pwc.com/us/en/industries/health-industries/library/pharma-life-sciences-deals-outlook.html

From the JP MorgAN Healthcare Conference

Deals Or No Deals, J.P. Morgan Sets The Tone For 2022

Collaborations, Not M&A, Dominate

  • 12 Jan 2022
·         OPINION
  • Mandy Jackson

Mandy Jackson@ScripMandy Mandy.Jackson@informausa.com

Executive Summary

No big buyouts were revealed during the annual J.P. Morgan Healthcare Conference for a third year in a row. Big pharma firms are in acquisition mode, but execs stress desire for easy integrations and scientific alliances. 

Biopharmaceutical industry players – and reporters – eagerly await merger and acquisition announcements going into the annual J.P. Morgan Healthcare Conference, hoping to scrutinize which big pharma is buying which other company for signs of what the deal-making environment will be like in the coming year. And in 2022, for the third year in a row, the meeting started with no big M&A deals.

Instead, Pfizer Inc.Novartis AGAmgen, Inc.Bristol Myers Squibb Company and others announced collaboration agreements. (Also see “Deal Watch: Bristol, Pfizer Lead Off J.P. Morgan Week With Two Deals Apiece” – Scrip, 11 Jan, 2022.)

They and their peers insisted during J.P. Morgan presentations and Q&A sessions as well as in interviews with Scrip that they do intend to invest in business development in 2022, but with a primary focus on smaller bolt-on acquisitions as well as licensing deals and collaboration agreements. Bolt-on deals have been the focus for the past few years. (Also see “The Pandemic Hurt, But EY Expects More Biopharma Deal-Making In 2021” – Scrip, 11 Jan, 2021.)

Amgen CEO Bradway On Deals: Good (Smaller) Opportunities Are Vast

By Mandy Jackson11 Jan 2022

Amgen is enthusiastic about deals of all sizes, including a new Arrakis collaboration, and is interested in large transactions like its Otezla buy – but Bradway said right-priced opportunities are fewer and farther between. 

Read the full article here 

While investors and others are clamoring for potential buyers to execute large transactions, Amgen CEO Robert Bradway made the astute – and as he pointed out, obvious – observation that there simply are more small, early-stage ventures to partner with than there are large, later-stage companies to acquire. Bradway also noted that while Amgen would like to buy another growing commercial-stage product like Otezla (apremilast), not only are few available but there are few assets at a price that still leaves value on the table for both companies’ investors.

Source: https://scrip.pharmaintelligence.informa.com/SC145698/Deals-Or-No-Deals-JP-Morgan-Sets-The-Tone-For-2022

Impact of New Regulatory Trends in M&A Deals

The following podcast from Pricewaterhouse Cooper Health Research Institute (called Next in Health) discusses some of the trends in healthcare M&A and is a great listen. However from 6:30 on the podcast discusses a new trend which is occuring in the healthcare company boardroom, which is this new focus on integrating companies that have proven ESG (or environmental, social, governance) functions within their organzations. As stated, doing an M&A deal with a company with strong ESG is looked favorably among regulators now.

Please click on the following link to hear a Google Podcast Next in Health episode

https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy5idXp6c3Byb3V0LmNvbS8xMjgyNjQ2LnJzcw?sa=X&ved=2ahUKEwil9sua2cf5AhUErXIEHaoTBQoQ9sEGegQIARAC

Other Related Articles on Life Sciences Investing Published in this Open Access Scientific Journal Include the Following:

Podcast Episodes by THE EUROPEAN VC
Tweets and Retweets by @pharma_BI and @AVIVA1950 for #NEVS at 2019 New England Venture Summit, December 4, 2019 at the Hilton in Boston, Dedham, MA, hosted by youngStartUp #NEVS
Leaders in Pharmaceutical Business Intelligence & youngStartup Ventures: Venture Summit Virtual Connect West, March 16th -18th 2021 featuring a dedicated Lifesciences / Healthcare Track  
Leader Profile: Family Offices – Impact Investing and Philanthropy – Health and the Life Sciences
37th Annual J.P. Morgan HEALTHCARE CONFERENCE: News at #JPM2019 for Jan. 10, 2019: Deals and Announcements
Real Time Coverage of BIO International Convention, June 3-6, 2019 Philadelphia Convention Center; Philadelphia PA

and  other related articles https://pharmaceuticalintelligence.com/page/3/?s=Life+Science+Investing

SOP for production of WordClouds for articles in the NEW GENRE Audio English-Spanish: BioMed e-Series – 18 Volumes in Medicine

Author: Aviva Lev-Ari, PhD, RN

LPBI Group’s SOP for production of WordClouds for articles in the NEW GENRE Audio English-Spanish: BioMed e-Series – 18 Volumes in Medicine https://pharmaceuticalintelligence.com/audio-english-spanish-biomed-e-series/

include the following steps:

  1. To master WordItOut.com
  2. To apply it to all the articles in the following e-Series: Series A: 6 volumes, Series B: two volumes, Series C: two volumes, Series D: four volumes, Series E: four volumes

How to Start?

In PART B of every Volume you will find the electronic Table of Contents (eTOCs) of the e-Book

EXCEPTIONS:

In Series C: Cancer Volume One, eTOCs is in A.2

In Series B: Genomics Volume Two eTOCs is in A.2

STEPS in Production of WordClouds for each article in an e-Book

1.  You sign in to WordItOut.com

2.  You review all the steps to produce a WordCloud from an MS Word File

3.  You click on the URL of the 1st article in Volume 1

4.  You copy the article into an MS Word File

5.  You use this file on WordItOut.com website to produce a WordCloud for the 1st article

6.  You edit the output by removing meaning less words like connective term: the a, an, all, some, more

7.  You RUN again on a file that does not include the terms REMOVED

8.  You select a Scheme of colors for background and for fonts – optimize contrast for visibility and legibility

9.  YOU MAINTAIN 8, above for all the articles in ONE volume

10.              YOUR FINAL WordCloud for ONE article you upload to the Media Gallery on our Website. You write as Legend Based on Article Title: Quote here Title. Produced on date by your name

11.              You go to the 1st article you ADD Media, this WordCloud you had produced BELOW the NAME of the Author, Curator, Reporter. YOU UPDATE the article with your WordCloud. You View Page for QA

12.              You move to repeat all of the above for 2nd article in the same volume

13.              When you complete ONE volume you announce that Volume X has all the WordClouds in it

14.              You move to other Volumes in the series you are working on. If it is Series A, then you continue with Volumes Two, Three, Four, Five, Six

15.              YOU START WITH VOLUME ONE AND LET ME KNOW how many hours it took to create all the wordClouds, N=number of articles in Volume One

16.              We will decide regarding other Volumes in the same series

Cardiothoracic surgeons at UC San Francisco performed the first robotically assisted mitral valve prolapse surgery in San Francisco.

Reporter: Aviva Lev-Ari, PhD, RN

Mitral valve surgery is performed when the heart’s mitral valve needs to be repaired. Traditionally, mitral valve surgery required opening the chest and putting the patient on heart-lung bypass to keep blood circulating during surgery. Since 2016, UCSF surgeons have been performing minimally invasive mitral valve surgery without having to open the sternum and with smaller incisions. Robotically assisted mitral valve surgery adds yet another level of precision.

“Robotically assisted mitral valve surgery allows us to make even smaller incisions with greater precision,” said Tom C. Nguyen, M.D., robotic heart surgeon and chief of Cardiothoracic Surgery at UCSF. “By using the robotic arms, we have more degrees of articulation than with our natural wrists. The robot also magnifies the surgical field 10X in 3D. Ultimately, this translates into more precise surgery with faster recovery.”

During the robotically assisted surgery, the surgeon looks through a 3D camera to see the mitral valve as well as other structures inside the heart. The surgeon uses the robotic surgical system to guide the robotic arms and movements of the surgical instruments.

“Every valve looks different, and the extraordinary 3D vision that the robot camera provides, is just a real step up from all the technologies we have been using in the past,” said Tobias Deuse, M.D., cardiac and transplant surgeon and director of Minimally-invasive Cardiac Surgery. “The camera, together with the increased mobility of the instruments, allows for a very thorough evaluation of the valve and helps us make good and long-lasting repairs.”

Thanks to these innovations, mitral valve patients have fewer complications and can be discharged within three-to-four days. This patient’s symptoms included increased fatigue and palpitations. Since the surgery, he is at home and his recovery is going well.

In addition to mitral valve surgery, there are plans for additional robotically assisted cardiothoracic surgeries, including removal of intracardiac tumors and myxomas as well as for coronary revascularization.

SOURCE

https://www.universityofcalifornia.edu/news/ucsf-performs-first-robotic-cardiac-surgery-san-francisco?utm_source=fiat-lux&utm_medium=internal-email&utm_campaign=article-general&utm_content=text

Other robotic surgeries currently being performed at UCSF

encompass a wide range of specialties and procedures, including:

  • removing cancerous tissue from the lungs, uterus, ovaries, colon, rectum, esophagus, bladder, prostate, head and neck, liver and pancreas. Other robotic surgeries are used for
  • the treatment of uterine fibroids and endometriosis, female pelvic organ prolapse repairs,
  • hernia repairs and
  • bariatric surgery.

Other related articles on Mitral Valve Repair published in this Open Access Online Scientific Journal include the following:

TricValve Transcatheter Bicaval Valves System – Interventional cardiologists at Cleveland Clinic have successfully completed the first implantation in North America

Reporter: Aviva Lev-Ari, PhD, RN

The Patient for this historic procedure:

An 82-year-old man presenting with severe symptomatic tricuspid regurgitation (TR) and right heart failure (RHF).

Expert Opinion: The Voice of Dr. Justin D. Pearlman, MD, PhD, FACC

https://pharmaceuticalintelligence.com/2022/04/20/tricvalve-transcatheter-bicaval-valves-system-interventional-cardiologists-at-cleveland-clinic-have-successfully-completed-the-first-implantation-in-north-america/

and another 64 articles

https://pharmaceuticalintelligence.com/?s=Mitral+valve

Explanation on “Results of Medical Text Analysis with Natural Language Processing (NLP) presented in LPBI Group’s NEW GENRE Edition: NLP” on Genomics content, standalone volume in Series B and NLP on Cancer content as Part B New Genre Volume 1 in Series C

NEW GENRE Edition, Editor-in-Chief: Aviva Lev-Ari, PhD, RN

Series B: Frontiers in Genomics Research NEW GENRE Audio English-Spanish

https://pharmaceuticalintelligence.com/audio-english-spanish-biomed-e-series/new-genre-audio-english-spanish-series-b-frontiers-in-genomics-research/new-genre-volume-two-latest-in-genomics-methodologies-for-therapeutics-gene-editing-ngs-and-bioinformatics-simulations-and-the-genome-ontology-series-b-volume-2/

PART A: The eTOCs in Spanish in Audio format AND the eTOCs in Bi-lingual format: Spanish and English in Text format

PART C: The Editorials of the original e-Books in English in Audio format

However,

PART B: The graphical results of Machine Learning (ML), Deep Learning (DL) and Natural Language Processing (NLP) algorithms AND the Domain Knowledge Expert (DKE) interpretation of the results in Text format – PART B IS ISSUED AS A STANDALONE VOLUME, named

https://pharmaceuticalintelligence.com/audio-english-spanish-biomed-e-series/new-genre-audio-english-spanish-series-b-frontiers-in-genomics-research/genomics-volume-2-results-of-medical-text-analysis-with-natural-language-processing-nlp/

 See only Graphic results in

Genomics, Volume 3: NLP results – 38 or 39 Hypergraph Plots and 38 or 39 Tree diagram Plots by Madison Davis

https://pharmaceuticalintelligence.com/biomed-e-books/genomics-orientations-for-personalized-medicine/genomics-volume-2-nlp-results-38-or-39-hypergraph-plots-and-38-or-39-tree-diagram-plots-by-madison-davis/

Series C: e-Books on Cancer & Oncology NEW GENRE Audio English-Spanish

https://pharmaceuticalintelligence.com/audio-english-spanish-biomed-e-series/new-genre-audio-english-spanish-series-c-e-books-on-cancer-oncology/new-genre-volume-one-cancer-biology-and-genomics-for-disease-diagnosis-series-c-volume-1%ef%bf%bc/

PART A:

PART A.1: The eTOCs in Spanish in Audio format AND

PART A.2: The eTOCs in Bi-lingual format: Spanish and English in Text format

PART B:

The graphical results of Medical Text Analysis with Machine Learning (ML), Deep Learning (DL) and Natural Language Processing (NLP) algorithms AND the Domain Knowledge Expert (DKE) interpretation of the results in Text format

See only graphics in

https://pharmaceuticalintelligence.com/biomed-e-books/series-c-e-books-on-cancer-oncology/cancer-volume-1-nlp-results-12-hypergraph-plots-and-12-tree-diagram-plots-by-madison-davis/

PART C:

The Editorials of the original e-Book in English in Audio format

Sperm damage and fertility problem due to COVID-19

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

Many couples initially deferred attempts at pregnancy or delayed fertility care due to concerns about coronavirus disease 2019 (COVID-19). One significant fear during the COVID-19 pandemic was the possibility of sexual transmission. Many couples have since resumed fertility care while accepting the various uncertainties associated with severe acute respiratory syndrome coronavirus 2 (SARS-Cov2), including the evolving knowledge related to male reproductive health. Significant research has been conducted exploring viral shedding, tropism, sexual transmission, the impact of male reproductive hormones, and possible implications to semen quality. However, to date, limited definitive evidence exists regarding many of these aspects, creating a challenging landscape for both patients and physicians to obtain and provide the best clinical care.

According to a new study, which looked at sperm quality in patients who suffered symptomatic coronavirus (COVID-19) infections, showed that it could impact fertility for weeks after recovery from the virus. The data showed 60% COVID-19 infected men had reduction in sperm motility and 37% had drop in sperm count, but, 2 months after recovery from COVID-19 the value came down to 28% and 6% respectively. The researchers also of the view that COVID-19 could not be sexually transmitted through semen after a person had recovered from illness. Patients with mild and severe cases of COVID-19 showed similar rate of drop in sperm quality. But further work is required to establish whether or not COVID-19 could have a longer-term impact on fertility. The estimated recovery time is three months, but further follow-up studies are still required to confirm this and to determine if permanent damage occurred in a minority of men.

Some viruses like influenza are already known to damage sperm mainly by increasing body temperature. But in the case of COVID-19, the researchers found no link between the presence or severity of fever and sperm quality. Tests showed that higher concentrations of specific COVID-19 antibodies in patients’ blood serum were strongly correlated with reduced sperm function. So, it was believed the sperm quality reduction cause could be linked to the body’s immune response to the virus. While the study showed that there was no COVID-19 RNA present in the semen of patients who had got over the virus, the fact that antibodies were attacking sperm suggests the virus may cross the blood-testis barrier during the peak of an infection.

It was found in a previous report that SARS-CoV-2 can be present in the semen of patients with COVID-19, and SARS-CoV-2 may still be detected in the semen of recovering patients. Due to imperfect blood-testes/deferens/epididymis barriers, SARS-CoV-2 might be seeded to the male reproductive tract, especially in the presence of systemic local inflammation. Even if the virus cannot replicate in the male reproductive system, it may persist, possibly resulting from the privileged immunity of testes.

If it could be proved that SARS-CoV-2 can be transmitted sexually in future studies, sexual transmission might be a critical part of the prevention of transmission, especially considering the fact that SARS-CoV-2 was detected in the semen of recovering patients. Abstinence or condom use might be considered as preventive means for these patients. In addition, it is worth noting that there is a need for studies monitoring fetal development. Therefore, to avoid contact with the patient’s saliva and blood may not be enough, since the survival of SARS-CoV-2 in a recovering patient’s semen maintains the likelihood to infect others. But further studies are required with respect to the detailed information about virus shedding, survival time, and concentration in semen.

References:

https://www.euronews.com/next/2021/12/21/covid-can-damage-sperm-for-months-making-it-harder-to-conceive-a-baby-a-new-study-finds

https://www.fertstert.org/article/S0015-0282(20)32780-1/fulltext

https://www.fertstertreviews.org/article/S2666-5719(21)00004-9/fulltext

https://www.fertstertscience.org/article/S2666-335X(21)00064-1/fulltext

https://www.fertstert.org/article/S0015-0282(21)02156-7/fulltext

https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2765654/

https://www.fertstert.org/article/S0015-0282(21)01398-4/fulltext

https://www.euronews.com/next/2021/08/27/do-covid-vaccines-affect-pregnancy-fertility-or-periods-we-asked-the-world-health-organiza

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

Infertility is a major reproductive health issue that affects about 12% of women of reproductive age in the United States. Aneuploidy in eggs accounts for a significant proportion of early miscarriage and in vitro fertilization failure. Recent studies have shown that genetic variants in several genes affect chromosome segregation fidelity and predispose women to a higher incidence of egg aneuploidy. However, the exact genetic causes of aneuploid egg production remain unclear, making it difficult to diagnose infertility based on individual genetic variants in mother’s genome. Although, age is a predictive factor for aneuploidy, it is not a highly accurate gauge because aneuploidy rates within individuals of the same age can vary dramatically.

Researchers described a technique combining genomic sequencing with machine-learning methods to predict the possibility a woman will undergo a miscarriage because of egg aneuploidy—a term describing a human egg with an abnormal number of chromosomes. The scientists were able to examine genetic samples of patients using a technique called “whole exome sequencing,” which allowed researchers to home in on the protein coding sections of the vast human genome. Then they created software using machine learning, an aspect of artificial intelligence in which programs can learn and make predictions without following specific instructions. To do so, the researchers developed algorithms and statistical models that analyzed and drew inferences from patterns in the genetic data.

As a result, the scientists were able to create a specific risk score based on a woman’s genome. The scientists also identified three genes—MCM5, FGGY and DDX60L—that when mutated and are highly associated with a risk of producing eggs with aneuploidy. So, the report demonstrated that sequencing data can be mined to predict patients’ aneuploidy risk thus improving clinical diagnosis. The candidate genes and pathways that were identified in the present study are promising targets for future aneuploidy studies. Identifying genetic variations with more predictive power will serve women and their treating clinicians with better information.

References:

https://medicalxpress-com.cdn.ampproject.org/c/s/medicalxpress.com/news/2022-06-miscarriage-failure-vitro-fertilization-genomic.amp

https://pubmed.ncbi.nlm.nih.gov/35347416/

https://pubmed.ncbi.nlm.nih.gov/31552087/

https://pubmed.ncbi.nlm.nih.gov/33193747/

https://pubmed.ncbi.nlm.nih.gov/33197264/

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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