Tag: Genomic

Research reveals potential target for enfortumab vedotin therapy in urothelial carcinoma

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Under the leadership of PD Dr. Niklas Klümper, Assistant Physician at the Department of Urology at the University Hospital Bonn (UKB) and Clinician Scientist of the BMBF-funded ACCENT program and PD Dr. Markus Eckstein, senior physician at the Institute of Pathology at the Uniklinikum Erlangen of the Friedrich-Alexander-University Erlangen-Nürnberg (FAU), an interdisciplinary research team has published new findings that indicate which patients with advanced urothelial carcinoma could benefit in particular from the new targeted therapy with the antibody-drug conjugate enfortumab vedotin. The study, published yesterday in the prestigious Journal of Clinical Oncology, identifies NECTIN4 amplification as a promising genomic biomarker for predicting treatment response to enfortumab vedotin. These findings could represent a significant advance in the improved treatment of this cancer.

As an alternative to chemotherapies used to treat aggressive advanced and metastatic urothelial carcinoma, a new class of drugs, known as antibody-drug conjugates, has recently become available. Enfortumab vedotin (EV) is the first drug in this new class to be approved by the EMA at for the treatment of patients and patients with metastatic urothelial carcinoma. Given the extremely promising results of the EV-302 trial, which showed a near doubling of survival with the combination therapy of EV and pembrolizumab, an immune checkpoint inhibitor, compared to conventional platinum-based chemotherapy in untreated patients with metastatic urothelial carcinoma, it is expected that the use of EV will increase significantly in the future.

Modern targeted oncology therapy

Antibody-drug conjugates consist of an antibody directed against a target structure on tumor cells and combined with a highly toxic chemotherapeutic agent. This combines the selectivity of targeted antibody therapy with the cytotoxic potential of conventional chemotherapy, which represents an innovative and new oncological therapeutic approach.

Research for more targeted therapy: precision oncology

Long-term efficacy of the new drug EV has so far been shown in an uncharacterized group of patients with metastatic urothelial carcinoma. The research team led by PD Dr. Niklas Klümper (UKB) and PD Dr. Markus Eckstein (Uniklinikum Erlangen) therefore wanted to analyze in more detail which patients benefit effectively from EV therapy in order to be able to use it in a more targeted manner – and conversely to identify patients who benefit less or not from EV, as they could possibly be treated more effectively with other therapies.

Nectin-4, the target structure of EV, is localized on chromosome 1q23.3. This gene segment is increased in about 20-25 percent of urothelial carcinomas, which is referred to as amplification. The new study aimed to investigate NECTIN4 amplifications as a potential genomic biomarker to predict treatment response to the drug EV in patients with advanced urothelial carcinoma.

“We have successfully developed and applied a simple FISH test (fluorescence in situ hybridization) that is specific for NECTIN4. This test proved to be a reliable method for identifying NECTIN4 amplification. Our studies showed that the presence of NECTIN4 amplification is a robust biomarker for response to EV therapy. In fact, over 90 percent of patients with NECTIN4 amplification showed tumor response to EV therapy, compared to about 30 percent of patients without this amplification”, says PD Dr. Markus Eckstein. These new findings can help to better select patients for this promising therapy in the future. “NECTIN4 amplification is a promising biomarker for predicting treatment response to EV. Excitingly, NECTIN4 amplification is also common in other solid tumors besides urothelial carcinoma, e.g. lung and breast cancer. The consideration of NECTIN4 amplification could therefore also be an exciting option for other tumor types in order to select patients for anti-NECTIN4-directed therapy in a more targeted manner. Further studies on this topic are needed, but our work could be the starting signal for the establishment of new targeted treatment strategies “, says PD Dr. Niklas Klümper.

Both study PIs also agree that without the great support of all the colleagues involved from the numerous oncology centers in Germany, Austria, the Netherlands and the USA, and of course without the patients’ consent to participate in the study, it could never have been carried out successfully.

The study was funded and initiated by the German Research Foundation (DFG) as part of the DFG Young Investigator Academy UroAgeCare of the German Society of Urology (DGU). “This underlines the high relevance of funding clinician scientist programs for medical progress,” says Prof. Michael Hölzel, mentor of PD Dr. Klümper within the program.

Source:

University Hospital Bonn (UKB)

Journal reference:

Klümper, N., et al. (2024) NECTIN4 Amplification Is Frequent in Solid Tumors and Predicts Enfortumab Vedotin Response in Metastatic Urothelial Cancer. Journal of Clinical Oncology. doi.org/10.1200/JCO.23.01983.

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April 25, 2024
Vaccines targeting chronic diseases show promise in combatting age-related conditions

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In a recent review published in Nature Aging, researchers explored vaccine-based therapeutics for age-related disorders.

Study: Targeting aging and age-related diseases with vaccines. Image Credit: Ground Picture/Shutterstock.com

Background

Aging is a primary risk factor for chronic illnesses, marked by reduced physiological capabilities. Cell senescence, genomic instability, stem cell fatigue, and mitochondrial failure are characteristics.

Aging also increases the risk of chronic illnesses such as Alzheimer’s disease, atherosclerosis, osteoarthritis, type 2 diabetes, chronic obstructive pulmonary disease (COPD), and cancer. Healthy habits like calorie control and regular physical exercise help prevent age-related disorders.

However, small-molecule therapies have limits, and vaccines provide a potential technique to target specific antigens to generate immune responses.

About the review

In the present review, researchers present new developments in vaccines using senescent cells to target the etiological agents of aging and related diseases.

Immunology of senolytic vaccines that target aging

Vaccines stimulate the innate immunological system, making it rapidly respond to infection. This reaction activates adaptive immune cells, causing humoral antibodies to manufacture antibodies and cell-mediated immunity to attack infected cells. Vaccinations lead to pathogen-targeted memory cell development to accelerate response to reinfections.
Vaccines targeting microbes, cell populations, or chemicals can prevent and treat disease development. Senolytic vaccines, which target senescent cells, have been demonstrated to reduce arterial plaque development.

These vaccination techniques provide new pathways for managing age-associated disorders, with advantages such as fewer injections, increased patient adherence, cost-effectiveness, and improved targeting efficiency.

Senolytic vaccinations target senescent cells by targeting chemicals on their surfaces, using peptide-based platforms to eradicate them through complement-dependent cytotoxicity (CDC) or natural killer (NK) cell-mediated and antibody-dependent cell-mediated cytotoxicity (ADCC).

Membrane proteins overexpressed in senescent cells are used as vaccine antigens or immune cell targets to stimulate the development of specific antibodies.

Tumor-associated antigens (TAAs) and tumor-specific antigens (TSAs) trigger a cluster of differentiation 4-expressing helper T cells, CD8+ cytotoxic T cells, and B cells to kill cancer cells.

Cancer vaccines use cell-based, virus-based, peptide-based, and nucleic acid-based platforms to stimulate adaptive immunity.

Research on vaccine-based strategies for age-related disorders

Alzheimer’s disease (AD) vaccinations attempt to lower the brain’s amyloid-beta (Aβ) and tau protein levels by stimulating the adaptive immune system to produce antibodies. Peptides with neuroprotective properties are potentially possible therapies.

Vaccines like ACI-24, UB-311, AV-1959D, ABvac40, ACI-35, AADvac1, and GV1001 target Aβ and tau proteins in innate immune cells. ACI-24 targets Aβ1-15 liposomes, UB-311 targets Aβ protein, AV-1959D targets deoxyribonucleic acid (DNA), ABvac40 targets Aβ protein, ACI-35 targets tau protein accumulation, and AADvac1 and GV1001 demonstrate long-term safety, tolerance, and immunogenicity.

Type 2 diabetes vaccinations target molecules like dipeptidyl-peptidase 4 (DPP4) and interleukin-1 beta (IL-1β) to restore levels and prevent problems.

The vaccines use peptide sequences to produce anti-DPP4 antibodies, increase glucose tolerance, restore beta cell mass, and reduce IL-1β production. They also couple prorenin epitopes with keyhole limpet hemocyanin (KLH), improving retinal blood circulation, decreasing microglia activation, and reducing gliosis and vascular leakage in diabetic rats.

Vaccines for age-related vascular diseases such as hypertension, abdominal aortic aneurysm (AAA), and atherosclerosis target molecules that regulate blood pressure, cholesterol, and blood vessel function. PMD-2850, PMD-3117, CYT006-AngQb, AT1R, ATRQβ-001, and ADR-004 inhibit angiopoietin 1 (Ang I) and age-related accumulation in hypertensive rats.

Vaccines containing KLH and Ang II decreased macrophage aggregation in the AAA wall, suppressed tumor necrosis factor (TNF) expression, and protected against elastic fiber injury.

The nerve growth factor (NGF) protein is an osteoarthritis target. Researchers covalently linked recombinant NGF proteins to virus-like particles (VLPs) derived from a cucumber mosaic virus with tetanus toxoid epitopes.

Vaccinated mice developed measurable antibodies against NGF and showed reversed pain behavior. ADAM metallopeptidase domain 12 (ADAM12) and GLI family zinc finger 1 (GLI1) levels are associated with fibrosis. Lentiviral vectors that encode these proteins decrease fibrotic activity in mice.

Proprotein convertase subtilisin/kexin type 9 (PCSK9) can treat fibrosis. PCSK9Qβ-003, an epitope peptide, enhanced kidney fibrosis, and increased fatty acid beta-oxidation-associated variables among Ldlr+/− murine animals. The vaccine can treat kidney fibrosis, hypercholesterolemia, and atherosclerosis.

Conclusions

Based on the review findings, senescent cells play a significant role in age-related chronic disorders and demonstrate immunogenicity, making them candidates for targeted vaccine elimination.

However, vaccinations can cause adverse effects such as injection site redness, discomfort, fever, and headaches. Continuous evaluation of vaccination safety is required to comprehend long-term adverse effects.

Vaccines targeting key mediators in age-related disorders have seldom proven efficacy in slowing disease development. Researchers must select antigens from key disease drivers or investigate epitopes generating robust immune responses to boost vaccination effectiveness.

Combinatorial therapy incorporating vaccinations and immunomodulatory medications may be more effective.

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April 17, 2024
Study reveals how SARS-CoV-2 hijacks lung cells to drive COVID-19 severity

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In a recent study published in the Journal of Experimental Medicine, researchers identified the cellular tropism and transcriptome consequences of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by infecting human lung tissue and using single-cell ribonucleic acid sequencing (scRNA-seq) to rebuild the transcriptional program in “infection pseudotime” for distinct lung cell types.

Lower respiratory infections, such as coronavirus disease 2019 (COVID-19), are a leading cause of death worldwide, producing pneumonia and acute respiratory distress syndrome. Understanding their early phases is difficult. Researchers used classical histopathological approaches and single-cell multi-omic profiling to infer early phases in human pathogenesis from lung lavage, biopsy, or autopsy materials. These approaches reveal a thorough picture of COVID-19 pneumonia at unparalleled cellular and molecular resolution, implying infection models including alveolar epithelium, capillaries, macrophages, and myeloid cells.

Study: Interstitial macrophages are a focus of viral takeover and inflammation in COVID-19 initiation in human lung. Image Credit: Dotted Yeti / Shutterstock

About the study

In the present study, researchers developed an experimental COVID-19 model to investigate early molecular processes and pathogenic mechanisms of SARS-CoV-2 infection at the cellular level in native tissues of the human lung.

The researchers established SARS-CoV-2’s cellular tropism and its unique and dynamic impacts on host cellular gene expression in specific types of lung cells. Prominent targets were lung-resident macrophages, of which one SARS-CoV-2 takes over transcriptomes, inducing a targeted host interferon (IFN) antiviral program, and several chemokines and pro-fibrotic and pro-inflammatory and cytokines signaling to various structural and immunological cells of the lung.

To determine the early stages of COVID-19 in human lungs, the researchers sliced lung tissue obtained from surgical specimens or organ donor individuals into thick sections and used them for tissue culture analysis. Subsequently, they exposed the tissues to the SARS-CoV-2 USA-WA1 2020 strain at 1.0 multiplicity of infection (MOI) for two hours before allowing the SARS-CoV-2 infection to continue for two to three days. They performed a plaque test on culture supernatants.

The researchers separated the slices and examined them by scRNA-seq to evaluate host and viral genetic expression during the SARS-CoV-2 infection. They also examined the viral RNA molecules’ junctional structure and processing by analyzing the scRNA-seq dataset with the SICILIAN framework. They used molecular atlas markers to distinguish lung cell types in healthy lung slices and measure viral RNA levels in infected cells.

The team performed multiplexed single-molecule fluorescence in situ hybridization (smFISH) to confirm lung cell tropism findings and show infected cells. They used single-cell gene expression patterns to identify cellular targets for inflammatory and pro-fibrotic signals elicited by the SARS-CoV-2 infection of a-IMs. They devised a technique for purifying macrophage populations from human lungs with a SARS-CoV-2 spike (S) protein-pseudotyped lentivirus (lenti-S-NLuc-tdT) to investigate lung macrophage entrance routes.

The researchers productively infected human lung slices cultivated ex vivo with SARS-CoV-2, with production rising between 24 and 72 hours of culture. They heat-inactivated, ultraviolet (UV)-treated, or administered 10.0 µM remdesivir, an RNA-dependent RNA polymerase inhibitor used as a COVID-19 therapeutic, to prevent viral stock infection.

Results

The analysis showed that SARS-CoV-2 preferentially infects active interstitial macrophages (IMs), which can amass hundreds of SARS-CoV-2 RNA molecules, comprising >60% of the cell transcriptome and producing dense viral RNA bodies. Infected alveolar macrophages (AMs) exhibit no severe reactions, with spike (S) protein-dependent viral entrance into AMs utilizing angiotensin-converting enzyme 2 (ACE2) and the cluster of differentiation 169 (CD169) and IM entry via CD209.

They found canonical sub-genomic junctions between the unusual sequence reads beyond their 39 terminal regions, indicating canonical-type SARS-CoV-2 messenger RNA (mRNA) production in the pulmonary cultures. They also found hundreds of new subgenomic junctions, showing a wide range of non-canonical and canonical sub-genomic SARS-CoV-2 RNAs produced during pulmonary infection.

Model of initiation, transition, and pathogenesis of COVID-19 and the viral lifecycle in AMs and IMs. (a–d) Model of COVID-19 initiation in the human lung and transition from viral pneumonia to lethal COVID-19 ARDS. (a) SARS-CoV-2 virion dissemination and arrival in the alveoli. Luminal AM encounter virions shed from the upper respiratory tract that enter the lung. AMs can express low to moderate numbers of viral RNA molecules and can propagate the infection but “contain” the viral RNA from taking over the total transcriptome and show only a very limited host cell inflammatory response to viral infection. (b) Replication and epithelial injury. SARS-CoV-2 virions enter AT2 cells through ACE2, its canonical receptor, and “replicate” to high viral RNA levels, producing infectious virions and initiating viral pneumonia. (c) a-IM takeover and inflammation signaling. SARS-CoV-2 virions spread to the interstitial space through either transepithelial release of virions by AT2 cells or injury of the epithelial barrier, and enter a-IMs. Infected a-IMs can express very high levels of viral RNA that dominate (“take over”) the host transcriptome and can propagate the infection. Viral takeover triggers induction of the chemokines and cytokines shown, forming a focus of inflammatory and fibrotic signaling. (d) Endothelial breach and immune infiltration. The a-IM inflammatory cytokine IL6 targets structural cells of the alveolus causing epithelial and endothelial breakdown, and the inflammatory cytokines recruit the indicated immune cells from the interstitium or bloodstream, which flood and infiltrate the alveolus causing COVID-19 ARDS. Local inflammatory molecules are amplified by circulating immune cells, and reciprocally can spread through the bloodstream to cause systemic symptoms of cytokine storm. (e) Comparison of the SARS-CoV-2 viral lifecycle in AMs and IMs. Although both can produce infectious virions, note differences in viral entry receptors (AMs can use ACE2 and CD169/SIGLEC1, whereas IMs use CD209); viral RNA transcription of dsRNA intermediates (greater in AMs); replication of full-length genomic RNA (greater in IMs); viral takeover, formation of RNA bodies, and induction of a robust host cell inflammatory response (only in IMs), and cell destruction/death (only in IMs).

Heat, UV-C inactivation, or remdesivir therapy prevented the development of canonical and non-canonical connections. The team observed SARS-CoV-2 takeover of an activated IM subtype in 176,382 cells with high-quality transcriptomes obtained from infected lung slices of four donor lungs and in 112,359 cells from mock-infected slices (cultured without viral addition) and 95,389 uncultured control cells (directly from freshly cut lung slices). A differential gene expression study of a-IMs over infection pseudotime revealed host gene expression alterations corresponding to SARS-CoV-2 RNA levels.

The study found that COVID-19 pneumonia infection and takeover cause an early antiviral cell response specific to activated interstitial macrophages, resulting in a powerful immunological and fibrotic signaling center. Inflammasome activation is uncommon and only detectable late in a-IM infection. Blocking antibodies against CD169 and CD209 prevented entrance into IMs and AMs. The study also highlighted IMs as the most vulnerable lung target, with initial emphasis on inflammation and fibrosis. Two unique molecular lineages of macrophage targets react differently to SARS-CoV-2, influencing etiology and treatments.

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April 15, 2024
Breakthrough study reveals melanoma’s resistance tactics to targeted therapy

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Melanoma is the deadliest form of skin cancer. With global incidence rates rising, new, more effective treatments are necessary to alleviate the health burden of the disease. Important advances in recent years include doctors using genetic tests to look for specific mutations they can target for more personalised, effective treatment.

Around 1 in 2 melanoma patients will have mutations in the BRAF gene. This gene normally makes a protein which helps control cell growth, but mutations can cause the cells to grow and divide uncontrollably instead, happening in many different types of cancer including melanoma.

The discovery of BRAF mutations has led to development of targeted therapies to inhibit its function. One of the standard treatment options for melanoma over the last ten years has been to simultaneously target both BRAF mutations and MEK. These two genes are part of the MAPK signalling pathway, which, in cancer, is rewired for uncontrolled growth. Targeting two different critical points in the same domino chain helps slow or stop cancer growth.

Despite great initial responses to the combined use of the first-generation inhibitors, around 50% of melanoma patients with BRAF mutations will relapse within one year. The cancer acquires resistance to the drugs, finding other ways to reactive the MAPK pathway through mechanisms which remain poorly understood.

Melanoma drug resistance is a huge clinical problem because it occurs in almost all BRAF-mutated patients under BRAF/MEK inhibitor therapy and there are few or no therapeutic alternatives. There is an urgent need to understand the many different underlying mechanisms and find new strategies to deal with this constantly evolving arms race.”

Dr. Francisco Aya Moreno, medically-trained oncologist and recent PhD graduate at the Centre for Genomic Regulation (CRG) in Barcelona

A study published today in the journal Cell Reports has disentangled the mechanisms behind one of the ways cancer cells develop resistance to targeted therapy. The study found that, in response to treatment, melanomas can ‘break’ parts of their BRAF gene, also known as genomic deletions. This helps the tumour create alternative versions of the protein (altBRAFs) which lack regions targeted by BRAF inhibitors, reactivating the MAPK pathway and making the drugs less effective. The finding was consistent across various lab models and patient tumour samples.

The findings are important because altBRAFs were thought to be made through alternative splicing, which is when cells use the same gene to synthesise different proteins. The discovery that genomic deletions, and not splicing, are the cause means a shift away from previous proposals for using drugs that target splicing as a therapeutic strategy.

“For years, we’ve known that some patients produce altBRAFs and these help the cancer resist treatment, but we misunderstood the mechanism behind their creation. Knowing that genomic deletions are the cause opens new avenues for developing therapies that could more effectively help patients with BRAF mutations,” explains ICREA Research Professor Juan Valcarcel, co-author of the study and researcher at the Centre for Genomic Regulation.

Surprisingly, the researchers found evidence of the same genomic deletions in melanomas which hadn’t been treated yet. In other words, melanomas can naturally develop mechanisms that mimic drug resistance, even without exposure to drugs. Identifying and targeting these early resistance mechanisms through profound genetic testing in a clinical setting before treatment begins could improve the efficacy of first-line therapies.

Even more surprisingly, further analyses revealed that genomic deletions might be a more widespread mechanism of oncogenesis and resistance than previously thought. Though uncommon, researchers found evidence of altBRAFs in melanomas with a normal-functioning BRAF gene, as well as in other types of cancer including non-small cell lung cancer, breast cancer, kidney cancer and prostate cancer. The findings could increase the patient population benefiting from targeted treatments which are currently under clinical development.

“There is an emerging class of drugs known as second generation RAF inibitors. Unlike BRAF inhibitors, these drugs have a broad spectrum, and so could potentially inhibit the function of altBRAFs. Clinical trials which are assessing their effectiveness should also expand to include melanoma patients with a normal functioning BRAF gene as well, and possibly to other cancer types which express altBRAFs,” explains Dr. Aya Moreno.

Dr. Aya Moreno is part of the second cohort of the PhD4MD programme, a joint effort by Centre for Genomic Regulation (CRG), the Institute for Research in Biomedicine (IRB Barcelona), the August Pi i Sunyer Biomedical Research Institute (IDIBAPS) and the Vall d’Hebron Research Institute (VHIR) designed to leverage the medical insight of a doctor to drive research that benefits patients.

“Having the opportunity to approach this research with both a clinician’s perspective and a scientist’s curiosity has been invaluable. It allowed us to uncover not just how melanomas resist treatment but also how this knowledge could lead to more effective therapies for patients. This fusion of clinical insight and scientific investigation is crucial for making real progress in our fight against cancer,” concludes Dr. Aya Moreno.

The study was led by Dr. Aya Moreno and co-supervised by Professor Juan Valcarcel at the Centre for Genomic Regulation and Dr. Ana Arance at IDIBAPS. It was also carried out in collaboration with Nuria López Bigas’ research group at IRB Barcelona. Since completing his PhD at the CRG, Dr. Aya Moreno has returned to the Medical Oncology department in the Hospital Clinic in Barcelona.

Source:

Center for Genomic Regulation

Journal reference:

Aya, F., et al. (2024). Genomic deletions explain the generation of alternative BRAF isoforms conferring resistance to MAPK inhibitors in melanoma. Cell Reports. doi.org/10.1016/j.celrep.2024.114048.

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April 13, 2024
Unveiling the key role of RNA modification in HIV-1 survival and replication

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A chemical modification in the HIV-1 RNA genome whose function has been a matter of scientific debate is now confirmed to be key to the virus’s ability to survive and thrive after infecting host cells, a new study has found.

This change to HIV-1 RNA, a tiny chemical modification on the adenosine building block of RNA known as m6A, is a common RNA editing process in all life forms that involves altering gene expression and protein production. The functional effect often represents a cellular solution but, in some cases, leads to disease.

By developing technological advances to observe a full length of HIV-1 RNA, researchers at The Ohio State University discovered the m6A modification occurs nearly exclusively at three specific locations on the HIV-1 RNA genome – out of the total 242 potential sites that can harbor an m6A – and these three m6As are crucial in viral replication. The finding suggested that redundancy was built into the system, and further analyses suggested that is, indeed, the case with HIV-1.

“These sites are very important for producing virus proteins and for producing viral genomic RNA,” said senior study author Sanggu Kim, associate professor of veterinary biosciences and an investigator in the Center for Retrovirus Research at The Ohio State University.

“An intriguing question is, why does HIV maintain multiple m6As? Our conclusion is that m6A is so important that HIV wants to have multiples to have redundancy. If it loses one or two, it’s OK. If it loses all three, it’s a problem.”

Though any drug development associated with this work is years away, Kim said the finding suggests targeting the site-specific m6A modifications could be the basis of designing an important new treatment for HIV infection.

The study is published today (April 11, 2024) in the journal Nature Microbiology.

HIV-1, the most common type of the human immunodeficiency virus, attacks immune cells and uses them to make copies of itself. An estimated 1.2 million people in the United States have HIV, according to the 2023 report from the Centers for Disease Control and Prevention.

The virus is a good example of why research on RNA modification has been getting a lot of attention in recent years, Kim said. Once thought of as the “middle guy” between DNA’s genes and life-sustaining proteins, RNA is now known to contain not just genetic information, but also to possess functional significance – in part because of the chemical modifications that accompany its messenger task.

Especially because HIV is an RNA virus with a very compact RNA genome, it has to encode all of the survival information within its RNA genome – it’s using not only nucleotide sequences, but all of the chemical and structural features of RNA as codes to execute its infection of host cells. We know every aspect of RNA function is very important, but we don’t really know how exactly these chemical and structural modifications of RNAs regulate virus infection.”

Sanggu Kim, associate professor of veterinary biosciences and investigator in the Center for Retrovirus Research at The Ohio State University

Though the m6A (short for N6-methyladenosine) modification was known to exist in HIV-1, previous studies had produced conflicting results about whether it helped or harmed the virus, primarily because its location was unknown and efforts to understand its effect were based on knocking out host cell genes rather than mutating the virus genome itself.

Kim and colleagues used – and refined – a technique called nanopore direct RNA sequencing to view a full length of HIV-1’s RNA genome, which is tricky to observe because RNA is a notoriously unstable and complex molecule.

The team first discovered the three m6A modifications and their specific locations. From there, the researchers analyzed individual RNA molecules with distinct ensembles of m6A modifications, including those with multiple m6As and those with just one of the three m6As. They found that any ensemble of m6A modifications, regardless of the number or the position of m6As, produced similar functional changes. Removal of all three, however, caused devastating effects to viruses – a dead giveaway that these m6As are redundant.

“Until now we didn’t know which exact nucleotides are modified and how they function, and how it’s important for viruses or how it’s important for cells. Our paper addresses the keys to these important questions,” Kim said.

“Why would HIV need all three modifications if they’re functioning in the same way?” he said. “Our study is the first to show that HIV-1 utilizes this unique, important mechanism at the RNA level for its evolutionary benefit.”

Almost all existing HIV drugs block virus replication, but no medications inhibit viral RNA and protein production. There is more to learn about the RNA modification in HIV-1, but Kim said the work hints at the potential to develop therapies that could target these later steps.

This research was funded by the National Institutes of Health, U.S. Department of Defense, U.S. Department of Energy and the C. Glenn Barber Fund Trust.

Co-authors include Alice Baek, Ga-Eun Lee, Sarah Golconda, Anastasios Manganaris, Shuliang Chen, Nagaraja Tirumuru, Hannah Yu, Shihyoung Kim, Christopher Kimmel, Olivier Zablocki and Matthew Sullivan of Ohio State, Asif Rayhan and Balasubrahmanyam Addepalli of the University of Cincinnati, and Li Wu of the University of Iowa.

Source:

The Ohio State University

Journal reference:

Baek, A., et al. (2024). Single-molecule epitranscriptomic analysis of full-length HIV-1 RNAs reveals functional roles of site-specific m6As. Nature Microbiology. doi.org/10.1038/s41564-024-01638-5.

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April 12, 2024
Baylor study reveals role of newly inherited DNA variants in recessive diseases

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You have your mother’s eyes and your father’s smile, but genetics is much more than just what’s on the surface. In a study that spans more than a decade, researchers at Baylor College of Medicine have looked at generations of families in a specific population to reveal the role newly inherited DNA variants play on recessive disease traits, and in the process, they have created a population specific database revealing unique DNA information unseen in larger cohorts.

The findings, now published in Genetics in Medicine OPEN, revealed a correlation between occurrences of complex genetic disorders in those families with increased levels of consanguinity when compared to unaffected populations. Consanguinity is when both parents contribute similar genetic markers to an offspring, such as by sharing a common ancestor, and the genetic information from both the genome inherited from the father and that from the mother are identical.

“We observed that the areas on the chromosome known as ROH, regions of homozygosity, were longer in those individuals in which there was a higher degree of parental consanguinity when compared to those with less,” said Dr. Zeynep Coban-Akdemir, postdoctoral associate in molecular and human genetics at Baylor and currently assistant professor at UTHealth School of Public Health as well as co-lead author on the study. “We can see what is happening when consanguinity is at play and also when new genetic variations are introduced into the family unit of the clan or tribe representing more distant ancestors.”

Dr. Xiaofei Song, a former Baylor graduate student now working as an assistant professor at Moffitt Cancer Center, said, “We further applied a statistical method to systematically assess the impact of these genetic variations on disease. Our results indicate that the newly introduced genetic variations can better explain the clinical features observed in our patients.” Song also is co-lead author on the study.

“The published study contributes to the field of both rare disease and population genomics. From a trainee perspective, the article provides a valuable resource for comprehending fundamental concepts of human genetics and applying diverse computational methods to elucidate these concepts,” said Ph.D candidate Tugce Bozkurt-Yozgatli, with the Acibadem University in Istanbul, Turkey.

Coban-Akdemir, who worked in the Lupski Lab at Baylor where the research was conducted, says this is an important part of the findings because it reveals how genes act within different populations and clans to contribute to different recessive genetic disorders.

The population studied was a cohort of individuals originating from Turkey that is known to have different variations in genetic markers when compared to other populations from greater Europe. Researchers created and analyzed a database of variants derived from exome sequencing, a genomics assay providing a glimpse into genetic variation genomewide, of 773 unrelated volunteers who were affected with various suspected rare Mendelian disease traits, which are diseases caused by a mutation in a single gene and clearly passed down from one generation to the next in accordance with Gregor Mendel expectations. They were compared to another database created by the same researchers of 643 unaffected relatives.

Roughly half of the genetic variants in this Turkish group are not present in greater European control populations that are found in shared databases commonly used by genetic researchers.

“This group of Turkish individuals and families gives us insight into genetics that the average population doesn’t provide. What we found in this Turkish population is very unique. Not only is this group underrepresented in larger databases, but it shows us that they have an enriched genetic variation that is only seen within this population when compared to European populations,” Coban-Akdemir said.

Dr. Davut Pehlivan, assistant professor of pediatrics – neurology at Baylor, said on a single individual there are around 40 million Watson-Crick base pair variations within our DNA.

“The Human Genome Project opened the doors for researchers to investigate entire genomic DNA complement using next-generation sequencing technology. However, more struggles appeared with these advancements. For example, it is hard to pinpoint which variant is causing disease among 40 million variations of our DNA. Studying healthy populations helps us to eliminate many of these common variations from consideration. Thus, we studied both patients and their healthy relatives in the Turkish population.” Pehlivan said. “There are a lot of changes in the genome, and we don’t fully understand the meaning of all of those details, but the data from this population study will help all investigators around the world who are trying to interpret the results of other variants in the human genome DNA.”

Pehlivan described gathering the information and families wanting to participate in genomics research beginning in 2010, traveling long distances to rural areas where the patients were mostly located, a human interest story itself, to make sure the database and clinical information would show an accurate representation for these families.

“We discovered more than 200 genes that contributed to the existing body of disease gene associations. This will help us get closer to understanding, in this population and in others, what is causing these diseases and the human biological perturbation underlying a broad scope of diseases. Our studies will open new avenues of research in human biology and genome biology and eventually help to potentially bring nucleic acid treatments, something used to develop the COVID vaccine, to the patients and families” Pehlivan said.

This team of researchers is not just helping the population that they studied, but their findings also can be applied to many populations. We all are very different individuals on this planet, yet our genes act very similarly, and we all share a common humanity. So, understanding how genetic disorders work helps us to support affected families across the globe.”

Dr. James R. Lupski, the Cullen Foundation Endowed Chair in Genetics and Genomics at Baylor

In the past, Coban-Akdemir and Dr. Claudia M.B Carvalho, previously with Baylor and currently in her own laboratory at the Pacific Northwest Research Institute (PNRI) in Seattle who also contributed to this study, have worked on studying variants of genes to identify causes of diseases through production of truncated or altered proteins that take on a new or different function. Their work also focused on databases of populations with and without genetic disease. Their current work reflects the importance of diversity and inclusion as work continues to reveal causes of genetic diseases.

This work was supported in part by the U.S. National Human Genome Research Institute /National Heart Lung and Blood Institute grant number UM1HG006542 to the Baylor Hopkins Center for Mendelian Genomics (BHCMG), the U.S. National Human Genome Research Institute U01HG011758 to the Baylor College of Medicine for the Genomics Research to Elucidate the Genetics of Rare Disease consortium (BCM-GREGoR), the National Institute of Neurological Disorders and Stroke Q22 (NINDS) R35NS105078, and the National Human Genome Research Institute U54-HG003273. J.E.P. was supported by NHGRI K08 HG008986.

Source:

Baylor College of Medicine

Journal reference:

Coban-Akdemir, Z., et al. (2024). The impact of the Turkish (TK) population variome on the genomic architecture of rare disease traits. Genetics in Medicine Open. doi.org/10.1016/j.gimo.2024.101830.

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April 10, 2024
Enhancer-gene mapping with SCENT method offers insights into disease mechanisms

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Genetic studies of diseases map segments of the genome driving disease. But to understand how those changes contribute to disease progression, it is important to understand how they may alter gene regulation of disease genes in cell populations assumed to be driving disease. “Enhancer-gene maps” link genomic regulatory regions to genes and are essential for understanding disease. But constructing them poses challenges due to limitations in current experimental methods, that make it difficult to apply the technique to rare cell populations and genes that only regulate specific cell types.

Researchers from Brigham and Women’s Hospital, a founding member of the Mass General Brigham healthcare system, have developed a statistical method called SCENT (single-cell enhancer target gene mapping). This method uses multimodal single-cell data to establish links between regulatory elements and genes, allowing them to pinpoint probable causal gene loci for both common and rare diseases. These insights might assist the development of treatments for various conditions.

The research team applied SCENT to nine multimodal single-cell datasets representing various human tissues, including immune, neuronal, and pituitary cells, aiming to understand the intricacies of DNA regulation in each specific cell type. With these data, they developed 23 distinct gene-enhancer maps, to investigate genetic variants and expression patterns associated with 1,143 diseases and traits. Notably, they discovered that, for immune diseases, crucial insights emerged not only from immune cells but also from cells within the affected tissues themselves.

For most autoimmune diseases, people assume that we need a general map of immune cells. But we find that the enhancer-gene maps of immune cells are different in affected disease tissues. We demonstrate how such a map can be used to interpret genetic data from rheumatoid arthritis and other autoimmune diseases.”

Soumya Raychaudhuri, MD, PhD, of the Brigham’s Division of Rheumatology, Immunology and Inflammation

Source:

Brigham and Women’s Hospital

Journal reference:

Sakaue, S., et al. (2024). Tissue-specific enhancer–gene maps from multimodal single-cell data identify causal disease alleles. Nature Genetics. doi.org/10.1038/s41588-024-01682-1.

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April 10, 2024
Understanding risks and prevention strategies
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In a recent scientific report published in the European Food Safety Authority (EFSA) journal, a large team of researchers from the EFSA and European Centre for Disease Prevention and Control (ECDC) discussed the intrinsic and extrinsic drivers for a potential pandemic due to evolved avian influenza viruses, and risk mitigation measures that are part of the One Health approach.

Report: Drivers for a pandemic due to avian influenza and options for One Health mitigation measures. Image Credit: Pordee_Aomboon / Shutterstock

Current avian influenza virus status

Wild bird populations in the European Economic Area (EEA) and the European Union (EU) are known to have a high prevalence of avian influenza viruses that cause significant disease and mortality. Outbreaks have also been reported from fur animal farms, where the avian influenza viruses are thought to have been transmitted from birds to mammals. These infections among fur animals are believed to be due to transmission of the virus from birds to various mammalian species and possibly also because of transmission between mammalian species.

Although cases of transmission of these viruses from birds to humans have not been widely reported, the evolution of avian influenza viruses and the dispersal of the virus through migratory wild birds could result in the selection of viruses that can infect humans.

Given that humans do not yet have robust immune defenses against avian influenza viruses, the emergence of a virus capable of infecting and rapidly spreading among humans poses the risk of a potential pandemic. Examining the intrinsic and extrinsic drivers that can facilitate the evolution of avian influenza viruses to infect humans and to develop effective mitigation measures is imperative.

Intrinsic and extrinsic drivers of viral evolution

Factors such as susceptibility of the host and viral characteristics, known as intrinsic drivers, and extrinsic drivers, such as environmental factors, human activities, and climate, can facilitate the emergence of avian influenza viruses that carry mutations that allow them to infect mammals.

Viral characteristics such as the reassortment propensity can drive the avian influenza virus to adapt to mammalian hosts. The hemagglutinin 5 neuraminidase 1 (H5N1) or avian influenza A virus, which contains the 2.3.4.4b clade that is currently circulating, has displayed evolutionary changes that could allow it to infect mammals and reassort. Furthermore, the global prevalence of the H5N1 virus in birds, including heterogenous poultry livestock, could result in the accumulation of various mutations that enable the virus to infect mammals, especially humans.

Reassortment can also lead to rapid genetic shifts that allow the virus to infect and replicate in humans and transmit among human populations. Coinfection of mammals with seasonal influenza and avian influenza virus could also increase the probability of reassortment events.

Furthermore, fur animals such as foxes and minks are highly susceptible to influenza viruses, and the exposure of these mammals to highly pathogenic strains of the avian influenza virus through contaminated feed could drive the virus’s adaptation to mammals. Outdoor production farms and those with proximity to areas rich in water birds provide more opportunities for the virus to be introduced into farms. Peri-urban and synanthropic wild animals could also facilitate the spread of the virus from wild birds to humans and animals.

Habitat destruction, extreme climatic events, and weather conditions can also impact the demography and ecology of these wild bird populations, acting as extrinsic drivers of the evolution of the avian influenza virus.

Mitigation measures

Risk mitigation measures included in the One Health approach suggested surveillance among target animal and human populations along with the generation and sharing of genomic data. Target animals included wild and captive birds, poultry, susceptible domestic mammals such as fur animals, cats, pigs, and peri-domestic and peri-urban mammals.

The measures also comprised development and access to sustainable, rapid diagnostic methods using genomic data to screen for avian influenza virus in relevant populations. An additional critical area for risk mitigation was occupational safety in areas where humans interact closely with target animals. Furthermore, reassortment risk can be reduced by vaccinating individuals with a higher probability of occupational exposure to avian influenza against the seasonal influenza virus.

The scientific report also discussed other areas, such as improving the veterinary infrastructure, biosecurity, communicating the risk to various audiences, and vaccinating animals, which could help mitigate the risk of the avian influenza virus adapting to humans and animals.

Conclusions

In summary, this report by the EFSA provided a detailed discussion of various intrinsic and extrinsic drivers, such as viral characteristics, factors that increase the susceptibility of animals, and environmental factors that could accelerate the adaptation of avian influenza viruses to mammalian hosts. The scientists also expanded on various mitigation measures, at individual and community levels, that could be followed to reduce the risk of adaptation and transmission of the avian influenza virus among animal and human populations.
Journal reference:

European Food Safety Authority (EFSA), European Centre for Disease Prevention and Control (ECDC), C., Adlhoch, C., Alm, E., Enkirch, T., Lamb, F., … Broglia, A. (2024). Drivers for a pandemic due to avian influenza and options for One Health mitigation measures. EFSA Journal, 22(4), e8735. DOI: 10.2903/j.efsa.2024.8735, https://efsa.onlinelibrary.wiley.com/doi/full/10.2903/j.efsa.2024.8735
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April 10, 2024
Research identifies how leukemia develops resistance to first line treatments

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Relapses in a common form of leukemia may be preventable following new research which has identified how the cancer develops resistance to first line treatments.

New research published in iScience by researchers from the University of Birmingham, the Institute of Cancer Research (ICR), Newcastle University, the Princess Maxima Centre of Pediatric oncology and the University of Virginia identified changes in a mutated form of acute myeloid leukemia (AML) samples from patients who relapsed after receiving FLT3 inhibitor treatment.

The team found that the resistant cancer had up-regulated multiple other signalling pathways to overcome the drug’s action, and that the genetic change was able to be replicated in lab tests.

These experiments revealed that by targeting RAS family proteins, using a small molecule inhibitor developed from a chemical library screen using the paratope of an inhibitory intracellular antibody by Terry Rabbitts’ team at the Weatherall Institute of Molecular Medicine University of Oxford and the ICR, increased signalling no longer rescued the cells from cell death.

The team identified that the transcription factors AP-1 and RUNX1 were at the heart of mediating drug resistance. The two factors cooperate and bind to their target genes together, but only in the presence of growth factor signalling. The drugs targeting FLT3 rewire the cell, resulting in the upregulation of other signalling pathway associated genes, which then restored AP-1 and RUNX1 binding. Drugging RAS, which is a key component in multiple signalling pathways, prevented this restoration of RUNX1 binding, and therefore signalling from growth factors no longer rescued the cancer cells from death.

Professor Constanze Bonifer from the Institute of Cancer and Genomic Sciences at the University of Birmingham, who has just taken up a position at the University of Melbourne, and is one of the senior authors of the paper said:

“The pharmaceutical industry had high hopes that drugs targeting aberrant growth factor receptors such as the FLT3-ITD would prevent people from relapse. However, cancer cells are smart, and rewire their growth control machinery to use other growth factors present in the body. Targeting RAS family members prevents the cancer from rewiring and using different signalling pathways to escape cell death.”

Targeting RAS blocks rewiring

The small molecule inhibitors used to target RAS in this study were developed using intracellular antibody technology. This technology involves screening a large number of antibody fragments to identify those which bind to the target protein in cells and prevent their protein-protein interactions. Small molecule inhibitors are can be screened from chemical libraries that interact with the parts of the target protein where these antibody fragments bind (the paratope). Due to the unparalleled natural specificity of these antibody fragments, this technology (called Antibody derived or Abd technology) can be used to target difficult to drug proteins and identify new parts of the protein which can be targeted to prevent protein-protein interactions.

Professor Terry Rabbitts from the Institute of Cancer Research who developed these drugs said:

“The strength of the Antibody-derived technology approach is that intracellular antibodies can selected to essentially any protein. In turn, their specific binding sites can be employed to select chemical compounds for drug discovery against hard to drug proteins. Mutant RAS was considered undruggable, but the Abd technology facilitated the development of the RAS-binding compounds used in the current study of cancer cell re-wiring. Abd technology will allow development of a new generation of drugs to hard-to-drug and intrinsically disordered proteins.“

AML with a FLT3-ITD mutation occurs in nearly 30% of all patients and is a highly aggressive disease with a poor prognosis. This genetic change causes the expression of a mutant growth factor receptor which is always active and therefore cancer cells expressing it grow uncontrollably. While inhibitors which specifically target the FLT3 protein are now in use in the clinic, patients treated with these inhibitors frequently relapse.

This work was funded by Leukaemia Research UK, the Medical Research Council, Blood Cancer Research UK, the Royal Society, the Wellcome and Cancer Research UK. The first author, Daniel Coleman is a John Goldman Fellow of Leukaemia UK.

Source:

Journal reference:

Daniel J.L., et al. (2024). Pharmacological inhibition of RAS overcomes FLT3 inhibitor resistance in FLT3-ITD+ AML through AP-1 and RUNX1. iScience. doi.org/10.1016/j.isci.2024.109576.

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April 9, 2024
Expanding research and clinical options for children with cancer

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Sponsored Content by TecanApr 8 2024

In this interview, Dr. Church, the Molecular and Pediatric Pathologist at Boston Children’s Hospital, talks to NewsMedical about their work in pediatric oncology, and the need to expand research and clinical options for children with cancer.

What inspired you to focus your work on pediatric oncology and the need to expand research and clinical options for children with cancer?

I have always been fascinated by biology and genetics, which drove my interest and pursuit of medicine and then pathology. As I moved through my training, I could clearly see the need for improved molecular techniques in pediatric oncology, and of course, it feels very compelling to be able to have a positive impact on a young life. It is such a privilege for me to work to support the care of children with cancer.

Image Credit: PeopleImages.com-Yuri A/Shutterstock.com

Could you share a specific story or accomplishment that stands out in your journey to advance pediatric oncology?

After many years of work developing and starting up our new molecular laboratory at Boston Children’s Hospital, we were able to design and validate a test to detect fusions in pediatric cancers. Soon after launching our test, we had a young boy who presented emergently to our hospital with metastatic tumors. We were able to use our new test to identify a gene fusion that clinched his diagnosis and made him eligible for a matched targeted therapy, and he responded beautifully to that treatment. More details about the case are available here.

In your role at Boston Children’s Hospital and Harvard Medical School, what innovative approaches have you introduced to improve the diagnosis and treatment of pediatric cancer?

We are fortunate to work closely with our colleagues in surgical pathology and pediatric oncology, so we’re able to see the needs of our team and our patients. We are focused on developing and implementing tests uniquely designed for children with cancers who have different genetic changes and different medical needs. Some of our tests include droplet digital PCR for children with brain tumors and vascular anomalies, RNA-based NGS assays for fusion detection in childhood cancers, sensitive DNA NGS for patients with vascular anomalies, and cell-free DNA assays for pediatric cancer patients.

Image Credit: Pixel-Shot/Shutterstock.com

The Profile and GAIN consortium studies have been significant in your work. Can you walk us through an example of how the findings from these studies directly impacted a child’s diagnosis and treatment?

Both studies enrolled cancer patients to receive molecular tumor profiling to help us understand how these new technologies can help our patients. The results are clear that this approach has a direct, meaningful impact on cancer care for both adult and pediatric patients. In our analysis of the GAIN study, 61% of pediatric cancer patients had genomic alterations with diagnostic significance, and 65% had alterations that inform potential matched targeted therapies.

What are the main challenges you see in pediatric oncology that you are working to address?

Challenges include the rarity of pediatric cancers and the lack of access to matched targeted therapies. Childhood cancers are rare overall but also represent a collection of rare and ultra-rare cancers, making it challenging to put together large datasets. We often look to other, more common cancers to help inform our decisions about how to care for children. Children are often left out of clinical trials for new treatments, which poses another barrier to improved care.

Tell us more about your collaborations with Tecan and how this partnership is shaping the landscape of clinical options for children with cancer.

I am grateful to Tecan for helping to communicate about molecular tumor profiling for children and for advocating for our pediatric cancer patients.

The NCI-funded Count Me In Study is quite significant. What outcomes or advancements are you hoping to achieve through this study, and what implications might it have for pediatric oncology?

Patients are increasingly interested in participating directly in research, particularly related to genetic sequencing, as it is so promising as a transformative technology.

With Count Me In, we have partnered with patients to design every aspect of the study and are returning genetic results directly to our patient participants. We hope to learn more about the genomic landscape of rare cancers (specifically osteosarcoma and leiomyosarcoma).

Image Credit: crystal light/Shutterstock.com

Our patient participants will also help us to understand how better to engage and partner with them and how to write genetic reports that are clear and that meet their needs.

As the Chair of Training & Education for the Association for Molecular Pathology, how are you preparing the next generation of pediatric oncology and molecular pathology experts to meet the field’s evolving needs?

I love working with residents and fellows who are our future leaders and experts in molecular diagnostics, both at the Association for Molecular Pathology and as the Program Director for the Harvard fellowship program. Our field is moving so quickly; we are providing the latest information but also helping to create a solid foundation of knowledge and confidence in their skills so that they are able to adapt to the changing needs of our patients over time.

Could you share a success story from your work, illustrating how molecular testing has made a tangible difference in a child’s cancer diagnosis and treatment?

I was fortunate to be involved in the care of a child with a large tumor that was unresectable with surgery. We discovered an NTRK fusion as the driver of his cancer, and our team was able to get him access to a new matched targeted therapy. He responded beautifully and was able to walk again.

https://blog.dana-farber.org/insight/2017/06/an-unclassified-tumor-with-a-precisely-targeted-therapy/

What, in your view, is the most promising avenue for future breakthroughs in pediatric oncology, and how does it align with your vision for the field?

Our pediatric pathologists and oncologists have become experts in molecular genetics and how to use those tests to help our patients. New drugs and technologies are coming out quickly – with continued support and collaboration, I expect we will make great strides in the next decade.

Image Credit: CI Photos/Shutterstock.com

In terms of community involvement, what can individuals, organizations, and the broader scientific and medical community do to support your mission of improving clinical options for children with cancer?

Awareness of the unique needs of patients and their families going through childhood cancer is so important. Please keep supporting organizations doing this work and advocating for improved access to molecular testing for children.

Where can readers find more information?

About Dr. Church

Dr. Church is a Molecular and Pediatric Pathologist at Boston Children’s Hospital, where she is a founder and associate medical director of the Laboratory for Molecular Pediatric Pathology (LaMPP). She is an Assistant Professor of Pathology at Harvard Medical School and the Program Director for the Harvard Molecular Genetic Pathology Fellowship, and the Chair of Training & Education for the Association for Molecular Pathology.

Her clinical and research work focuses on bringing molecular testing to the clinical care of children with cancer. Through institutional projects (the Profile study, GAIN consortium study), we have profiled thousands of children’s tumors and have used these results to make real-time impacts on their diagnoses and treatments. Dr. Church is also involved in national initiatives to improve the quality and access to molecular testing for children with cancer, including the NCI-funded Count Me In Study (Dana Farber, Broad Institute), the National Comprehensive Cancer Network, National Institutes of Health, and the Children’s Oncology Group.

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April 8, 2024