The Research Roundup - December 2021

Updated: Jun 15


The following is a high-level overview of medical papers and news articles, panned primarily for my own purposes to raise my level of knowledge and awareness of the current efforts in the fields of personal interest to me. This includes topics on conditions beyond HMs, such as solid cancers (for example prostate, breast, or colon), neurodegenerative conditions (such as Alzheimer's Disease), and of course technology (such as IT, Imaging, AI, and databases). Some of these I may later re-read to go a bit deeper regarding possible relevance or interest to CMPNRF. But even with this preliminary coverage, it is difficult not to notice some important observations:

  • We are living in a very much connected and interconnected world where there are, or may very well be, relevance in the research of Hematologic Malignancies (HMs) to be found in other areas, if one only has an open mind to possibilities.

  • We are living in a world of incredible change and rapid pace of change; we only came to understand a year ago that there is such a concept as mRNA vaccines for Covid, and just this month I read an article regarding a phase II study in a human, for an mRNA vaccine for cancer (colon cancer to be precise; by BioNTech). One year ago I did not have the foggiest idea what an mRNA was; this Christmas I received a gift of a book: Epigenetics, Nuclear Organization and Gene Function - With Implications of Epigenetic Regulation and Genetic Architecture for Human Development and Health . . . who woulda thunk!

  • We are living in a world where one cannot work (including medical research) without the latest technology at our fingertips and that keeping up with the changes in that arena are formidable (as I know all too well, after only a few months after retiring from consulting in that field, I now feel very much "well past my best before date")

This list of papers is not in any sequence (but all published recently, this month of December 2021) and I make only the smallest of comments, but perhaps there may be some gems for those with a voracious appetite for reading such things. . . enjoy. -Russ Hardy


[Note: Russ' comments are offset in gray, and research article exerpts are included in "quotes".]


 


I found this line of research (looking at some of the features of the Interactome, particularly related to cell differentiation processes) to be an interesting approach with perhaps some future applications to clinical treatments. The study was focused on AML, but perhaps may also be relevant to other HMs?

Biosensor barcodes identify, detail 'chatting' among cancer cells, by Johns Hopkins University School of Medicine November 30, 2021


"When cancer cells communicate, numerous proteins constantly change how they interact with one another," says senior study author Chuan-Hsiang (Bear) Huang, M.D., Ph.D., assistant professor of pathology at the Johns Hopkins University School of Medicine. "Studying this signaling in depth and in real time has traditionally been difficult, so we needed a method that could simultaneously image, track and analyze everything happening in the network, and therefore, reveal the true relationships among these activities."

"The AI analysis enables us to read the barcodes in seconds rather than hours, a crucial step toward seeing how the activity of different proteins are synchronized over time," says Chi.

"Using biosensor barcodes, we hope to get more insights and more comprehensive views than ever before of how oncogenes [genes that initiate the development of cancer cells] affect communication among cancer cells, and with other networks such as those used by the immune system," says Huang. "These findings could help direct new interventions and treatments.""


Changing the identity of cancer cells to eliminate them by University of Pennsylvania December 1, 2021 study, published in the journal Cancer Discovery


"The Study identifies an enzyme that regulates the process by which AML cells differentiate. In both cell lines and an animal model, the researchers found that inhibiting this enzyme, particularly in combination with other anti-cancer therapies, prompted AML cells to lose aspects of their identity associated with aggressive growth. The cells also began to exit the cell cycle, on the path toward maturing into a new cell type.

M. Andrés Blanco, an assistant professor at the University of Pennsylvania's lab is particularly interested in the epigenetic regulation of cell identity. One of the screened proteins that affected cell differentiation was KAT6A, an enzyme known as a histone acetyltransferase. As a histone acetyltransferase, KAT6A can add one of three different modifications to histones, proteins around which DNA winds. The finding helped the researchers understand that KAT6A is what's known as a "writer." It "writes" the modification of H3K9ac, and ENL is a "reader," taking in that modification and acting upon it."


KAT6A and ENL form an epigenetic transcriptional control module to drive critical leukemogenic gene expression programs Fangxue Yan, Jinyang Li, Jelena Milosevic, Ricardo Petroni, Suying Liu, Zhennan Shi, Salina Yuan, Janice M Reynaga, Yuwei Qi, Joshua Rico, Sixiang Yu, Yiman Liu, Susumu Rokudai, Neil Palmisiano, Sara E Meyer, Pamela J Sung, Liling Wan, Fei Lan, Benjamin A Garcia, Ben Z Stanger, David B Sykes and M. Andres Blanco

Cancer Discovery, December 1, 2021 DOI: 10.1158/2159-8290.CD-20-1459


"Abstract: Epigenetic programs are dysregulated in acute myeloid leukemia (AML) and help enforce an oncogenic state of differentiation arrest. To identify key epigenetic regulators of AML cell fate, we performed a differentiation-focused CRISPR screen in AML cells. This screen identified the histone acetyltransferase KAT6A as a novel regulator of myeloid differentiation that drives critical leukemogenic gene expression programs. We show that KAT6A is the initiator of a newly-described transcriptional control module in which KAT6A-catalyzed promoter H3K9ac is bound by the acetyllysine reader ENL, which in turn cooperates with a network of chromatin factors to induce transcriptional elongation. Inhibition of KAT6A has strong anti-AML phenotypes in vitro and in vivo, suggesting that KAT6A small molecule inhibitors could be of high therapeutic interest for mono or combinatorial differentiation-based treatment of AML" [emphasis added].




The following study was performed relating to solid tumor (specifically Non–small cell lung cancer (NSCLC)) . . . not being familiar with immunotherapies for HM’s, I was just wondering if there were similar immune responses and studies for HMs”

A reservoir of stem-like CD8+ T cells in the tumor-draining lymph node preserves the ongoing antitumor immune response September 11, 2021, Kelli A. Connolly et al, A reservoir of stem-like CD8 + T cells in the tumor-draining lymph node preserves the ongoing anti-tumor immune response, Science Immunology (2021). DOI: 10.1126/sciimmunol.abg7836


"To an immunologist, autoimmune diseases like Type 1 diabetes are the polar opposite of cancer. In the former, the immune system goes into overdrive and attacks the body's own organs in a relentless manner, eventually causing disease; with cancer, the immune system shuts down and fails to mount an aggressive attack to stop cancer from forming.

In a new study by Yale Cancer Center, researchers show stem-like T cells within certain lymph nodes could be natural cancer fighters. Targeting these T cells—which are a type of white blood cells—with immunotherapy drugs could increase the number of cancer patients that respond to treatment.

"T cells in tumors become exhausted, but our study results show the stem-like T cells within the nearby lymph nodes do not experience exhaustion during the course of disease," said Kelli A. Connolly, a post-doctoral fellow at Yale Cancer Center and lead author of the study. "This could be an important treatment advance as the potential to respond to immunotherapy is preserved."

This article was looking at unique methods to examine tissue samples; while the study dealt with breast cancer biopsy tissues, my question is could it be equally successful with bone marrow samples?

High-speed holography of cells spots physical beacons of disease November 30, 2021

Duke University. More information: Cindy X. Chen et al, Automated Classification of Breast Cancer Cells Using High-Throughput Holographic Cytometry, Frontiers in Physics (2021). DOI: 10.3389/fphy.2021.759142


"Biomedical engineers at Duke University have engineered a holographic system capable of imaging and analyzing tens of thousands of cells per minute to both discover and recognize signs of disease. In the proof-of-concept demonstration, the technique distinguished between healthy samples and either cancerous or carcinogen-exposed, pre-cancerous cells with nearly 100% accuracy, using just four basic cellular physical parameters out of a holographic panel of 25. The results point toward a promising screening or diagnostic technology that is simpler and cheaper to use than current standard practices, [emphasis added] making it a potential target for use in remote, low-resource settings. Holographic cytometry is an ultra-high throughput quantitative phase imaging modality that is capable of extracting subcellular information from millions of cells flowing through parallel microfluidic channels."

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This was a recent Canadian paper (yeah!). UdeM-affiliated Maisonneuve-Rosemont Hospital Research Center. This is a very detailed and very technical paperbut may be of some interest.

Researchers discover that proteasome molecules can join forces to prevent cancer

University of Montreal November 30, 2021. More information: Maxime Uriarte et al, Starvation-induced proteasome assemblies in the nucleus link amino acid supply to apoptosis, Nature Communications (2021). DOI: 10.1038/s41467-021-27306-4


"El Bachir Affar's team looked at a tiny biological machine called the proteasome that exists in every cell in the body. This machine is responsible for breaking down and removing unwanted, malformed or excess proteins, a vital process for the proliferation and normal functioning of the cells. In addition, this process ensures the recycling of amino acids, which are the basic building blocks that the cells use to make new proteins.

"This discovery is very exciting," said Maisonneuve-Rosemont oncologist Dr. Pierre Dubé. "Dr. Affar and his team have discovered a new process that when faulty, can contribute to cancer. This opens the way to a new field of study and could lead to the identification of molecular targets for the treatment of cancers."

“Here we show that the mammalian proteasome undergoes liquid-liquid phase separation in the nucleus upon amino acid deprivation. We termed these proteasome condensates SIPAN (Starvation-Induced Proteasome Assemblies in the Nucleus)”.

“Our data also suggest a link between SIPAN and tumor development/progression. First, certain cancer cells including T47D, PC3, MIA PaCa-2, have reduced ability to form SIPAN. Second, nutrient deprivation induces p53-dependent apoptosis with a notable upregulation of the p53 target gene NOXA; and inhibition of RAD23B and PSME3 prevents p53/NOXA upregulation and apoptosis. Third, we also found that oncogenic transformation of normal human fibroblasts results in reduced cell ability to form SIPAN and resistance to apoptosis induced by nutrient deprivation.”

This paper covers some of the impacts on transcription factors and interactions with other chromatin partners that if interrupted lead to reduced immunity actors such as T-cells

Germline biallelic mutation affecting the transcription factor Helios causes pleiotropic defects of immunity, Tala Shahin et all, Science Immunology, November 26, 2021.


“Helios is one member of the Ikaros family of transcription factors, a set of proteins that play critical roles in the differentiation and regulation of hematopoietic cells including lymphocytes. Mutations in Ikaros family members are associated with both hematological cancers and inborn errors of immunity”

“Binding of Helios with specific partners mediates this regulation, which is ultimately necessary for the transcriptional programs that enable T cell homeostasis in health and disease.”


This paper combines molecular biology with technology to image structures and provide insight as to how architecture impacts functions.

Stochastic chromatin p acking of 3D mitotic chromosomes revealed by coherent X-rays

Daeho Sung, Chan Lim, Masatoshi Takagi, Chulho Jung, Heemin Lee, Do Hyung Cho, J et al

PNAS November 16, 2021


“The structural link between meter-long DNA molecules and chromosomes a few microns in size and their highly space-effective and fault-free packing and unpacking mechanisms remain a puzzle. This research addressed this fundamental issue by resolving a three-dimensional (3D) structure of human chromosomes using cryogenic coherent X-ray diffraction tomography.

While supporting the structural analysis, molecular dynamics simulations further elucidate the critical role of short-range attraction between chromatins and DNA-binding proteins in forming micrometer-sized chromosomes.”


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This paper discusses the use of labelled peptides for imaging and probing radiotheranostics.

68Ga- and 211At-Labeled RGD Peptides for Radiotheranostics with Multiradionuclides

Kazuma Ogawa*, Hiroaki Echigo, Kenji Mishiro, Saki Hirata, Kohshin Washiyama, Yoji Kitamura, Kazuhiro Takahashi, Kazuhiro Shiba, and Seigo Kinuya Molecular Pharmaceutics 2021, 18, 9,


"In this study, we hypothesized that probes for radiotheranostics combined with multiradionuclides, such as 68Ga and 211At, have useful clinical applications. These results indicate the usefulness of these probes in radiotheranostics with multiradionuclides, such as a radiometal and a radiohalogen, and they could contribute to a personalized medicine regimen. [emphasis added]”

This paper introduces the current field of oncolytic irotherapy. While it appears to be related to solid cancers, who knows, it may also apply to HMs?

New review highlights cancer-crushing viruses More information: Masmudur M. Rahman et al, Oncolytic Viruses: Newest Frontier for Cancer Immunotherapy, Cancers (November 30, 2021)

"In a recent review article for the journal Cancers, Masmudur Rahman and Grant McFadden describe a class of viruses that act to combat rather than cause deadly disease. Such oncolytic viruses as they are known, have a remarkable ability to target and destroy cancer cells, while leaving healthy cells untouched. Today, a variety of oncolytic viruses are being explored for cancer therapy. While many such viruses can directly attack and terminate malignant cells, their primary strength may lie in their ability to alert an inactive or disabled immune system to the presence of cancer."

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This paper explores an example of using a mechanism to suppress a mutant gene. While it is specific to ALS and only for scenario of single mutation causation; it is instructive as to the process.

Clinical trial shows antisense oligonucleotide safely suppresses mutant ALS gene in pilot human study More information: Jonathan Watts, Suppression of mutant C9orf72 expression by a potent mixed backbone antisense oligonucleotide, Nature Medicine (December 23, 2021)


“Using a short, synthetic chain of chemically modified nucleotides engineered in the RNA Therapeutics Institute at UMass Chan Medical School, Robert H. Brown Jr., DPhil, MD, Jonathan Watts, Ph.D., and colleagues have shown the ability to suppress mutant forms of an ALS gene known as C9ORF72 in a single-patient pilot study. While other teams have documented that this gene can be suppressed in cells in culture, this is the first time this type of antisense oligonucleotide treatment for C9ORF72 ALS has been demonstrated in a person with ALS. Antisense oligonucleotides are short, synthetic, single-stranded oligonucleotides that can alter RNA and reduce, restore, or modify protein expression. The type of ASO used in this research prevents gene expression by binding to messenger RNA (mRNA) strands. Once this binding takes place, this hybrid sequence is targeted and naturally degraded by enzymes in the cell.”

This paper (again a marriage of technology to molecular biology) looks at how observing a process at atomic resolution and in part in real time using high-resolution nuclear magnetic resonance (NMR) spectroscopy can provide insight to why a process works in vitro but doesn’t work in vivo.

DNAzymes: How active DNA molecules with therapeutic potential work (Heinrich-Heine University Duesseldorf; More information: Manuel Etzkorn, Time-resolved structural analysis of an RNA-cleaving DNA catalyst, Nature (December 22, 2021)


"DNAzymes are precision biocatalysts that destroy unwanted RNA molecules. They comprise a catalytic core comprising around 15 nucleic acids flanked by short binding arms on the right- and left-hand sides, each with around ten nucleic acids. The aim is to target unwanted RNA molecules of viruses, cancer or damaged nerve cells, using DNAzymes to attack and destroy them. This is achieved via binding sequences that match a sequence of nucleotides on the targeted RNA molecule. We established that magnesium, as a key cofactor, plays various essential roles in the mechanism, but that it binds relatively poorly and only briefly to the DNAzyme. "

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This news article has a unique idea, to build a biologic computer (that is that can perform logic such as ”AND” gates (Input A AND Input B equals Output X) and “OR” gates (Input A OR Input B Equals Output Y ) to derive more complex markers of cancer cells; and then to insert said computer into a hollowed out virus.

With a ‘biological computer,’ scientists look to target cancer while sparing healthy cells

By Angus Chen Dec. 22, 2021


"Synthetic biologist Kobi Benenson might have a way around that (confusing cancer cells with healthy ones). Inside an engineered virus, he and his colleagues at ETH Zurich packaged a programmable genetic circuit that uses multiple targets to build a profile of a cancer cell.Most other cancer therapeutics only recognize targets that exist on the outside membranes of cells, but now microRNAs, proteins, and other intra-cellular molecules are available for engineering. The other feat was getting the “NOT” function to work, Wong said. Typically, cancer drugs only attack a cell when a target is present. That means, aside from allowing biological computers like this to build safety switches, it opens yet another entirely new way of getting drugs to recognize cancer cells."

This news article sheds some light on the complexity of interactions relating to malignancies, not just among mutations, but also among and in concert with other normal genes and molecules. This also could not be done without technology (in this case Network Modelling).

Homing in on shared network of cancer genes, Hartmut "Hucky" Land, Ph.D., deputy director of the Wilmot Cancer Institute and the Robert and Dorothy Markin Professor of Biomedical Genetics at the University of Rochester Medical Center Reported by Susanne Pallo, December 21, 2021


“Wilmot Cancer Institute researchers are a step closer to understanding the complex gene interactions that cause a cell to become malignant. In a new Cell Reports study published today, the group used network modeling to home in on a set of such interactions that are critical to malignancy, and likely to be fertile ground for broad cancer therapies. Targeting non-mutated proteins that are essential to making cells cancerous is a broader approach that could be used in multiple cancers," said Land, "but it's hard to find these non-mutated, essential genes."

This paper identifies the mechanism by which inhibitors of the ERK5 protein kinase impair the proliferation of cancer cells and induce their death. In the scenario where the cell’s endoplasmic reticulum becomes stressed, a process that can compromise the survival of cells.

Mechanism that impairs cancer cell proliferation and induces their death

Vall d'Hebron Research (VHIR) and the Universitat Autònoma de Barcelona (UAB), Dr Jose M Lizcano, Maria Casas, Idoia Bolinaga-Ayala, Dr. Nora Dieguez-Martínez, Sergio Espinosa-Gil and Dr. Göhkan Gorgisen December 21, 2021


“The results, obtained using human cancer cell lines, demonstrate that ERK5 inhibition activates cytotoxic autophagy, a process that triggers cancer cell death, without affecting healthy cells. A combination of ERK5 inhibitors and chemotherapy could improve cancer treatment. Stress within a cell can lead to UPR which in turn leads to a cytotoxic autophagy that activates apoptosis."

This news article shows the confluence of epigenetic research and studies on human aging.

A worm wide web: Scientists create network of age-related genes, by Babraham Institute December 21, 2021


“Researchers from the Babraham Institute's Epigenetics research program have published a map of genetic interactions in C. elegans in iScience which can be used to identify new genes that influence lifespan and that have equivalent genes in humans. The researchers found that most key genes for longevity belong to transcription factors and metabolic genes. Their results pinpointed 50 new genes linked to aging in worms identified, 43 of which have human equivalents.”

This study provided an exciting view into the use of technology and structural biology to derive a three dimensional, near atomic level of detail image that clarifies how Heme is transported across membranes of both Hemoglobin and Cytochrome proteins.

A pathway emerges: Biologists describe structure and function of a heme transport and assembly machine by Washington University in St. Louis, December 20, 2021 Robert Kranz, Cryo-EM of CcsBA reveals the basis for cytochrome c biogenesis and heme transport, Nature Chemical Biology (2021) DOI: 10.1038/s41589-021-00935-y. www.nature.com/articles/s41589-021-00935-y


“Heme transport is transient, which means heme moves through membranes quickly and leaves behind no traces. And heme-binding membrane proteins are difficult to purify in large quantities. They leveraged a cutting-edge structural biology technique called single particle averaging, which utilized a state-of-the-art cryo-Electron Microscope (cryo-EM) to image different views of the protein in its natively vitrified (frozen) state."



This paper (while primarily related to solid tumours) combines a modified DNA Sequencing Process with concepts of spatial location within and external to a cell, and also combined with mapping of epigenetic expressions.

New DNA sequencing technique preserves cells' locations within tissues

by Jessica Lau, Broad Institute of MIT and Harvard December 16, 2021 Tongtong Zhao et al, Spatial genomics enables multi-modal study of clonal heterogeneity in tissues, Nature (2021). DOI: 10.1038/s41586-021-04217-4


"Within complex tissues such as cancer tumors, individual cells can vary widely from each other. Internally, cancer cells can develop unique DNA mutations and genomic changes, potentially leading to drug resistance, metastasis, or relapse. Externally, the cells' specific locations within the tissue also matter since the local structure of a tumor and its surrounding tissues can affect cell state and drug permeability. Researchers developed a new technique of spatially resolved DNA sequencing, called slide-DNA-seq. When further combined with spatially resolved gene expression analysis, the technology gives researchers a better understanding of cancer progression and potential treatment."

Mayo Clinic cancer researchers have used mRNA therapies to detect and then to fix Immunotherapy problems patients have experienced with poor responses otherwise.

Research finds immune system responds to mRNA treatment for cancer

by Mayo Clinic Ti Wen et al, NKG7 is a T-cell intrinsic therapeutic target for improving antitumor cytotoxicity and cancer immunotherapy, Cancer Immunol Res (2021). DOI: 10.1158/2326-6066.CIR-21-0539 December 15, 2021


“One of the major obstacles in cancer treatment is the low response rate in patients who receive immune checkpoint inhibitors to prevent an immune response from being so strong that it destroys healthy cells in the body. Most patients with advanced cancers have not benefited from current immune checkpoint blockade therapy," says Dr. Dong. "Our study provides a tool (a monoclonal antibody) to detect this problem and also provides an mRNA-based therapy to fix it. “


This paper discusses the recent progress with blood tests measuring the detritus (DNA fragments) released into the blood system that result from the immune system activities. The immune system is very finely tuned to be in a state of homeostasis: not too weak but also not too strong. Any treatment that is accomplished via an immunotherapy process, is known to be all too well at risk of this homeostasis being compromised with perhaps serious un-intended consequences.

Blood test detects immune and inflammatory activity in tissues, without painful biopsies and expensive imaging by Hebrew University of Jerusalem, December 15, 2021

Ilana Fox-Fisher et al, Remote immune processes revealed by immune-derived circulating cell-free DNA. eLife. DOI: 10.7554/eLife.70520

Journal information: eLife


"Common blood tests that are only focused on blood cell counts are not able to detect immune activities in the body's remote tissues, such as those found in bone marrow, lymph nodes and other organs. This paper explores how they focused on two fundamental biological principles. First, dying cells release fragments of DNA into the blood stream. Second, the DNA of each cell type contains a unique chemical pattern called methylation.

The team found similar success with lymphoma, a type of cancer that usually doesn't show up in blood tests. However, the new blood test does pick up DNA fragments left by the immune system's fight with lymphoma, without the need for bone marrow aspiration and further imaging."

This paper has an interesting review of Metabolomics by matching a pharmacologic library to a range of phenotypical hematologic malignancies.

Specific metabolic dependencies of cancer cells revealed by perturbation with tailored chemical library by Austrian Academy of Sciences, December 14, 2021, Metabolic drug survey highlights cancer cell dependencies and vulnerabilities. Nature Communications (2021). DOI: 10.1038/s41467-021-27329-x Journal information: Nature Communications



"Metabolic reprogramming has thus been recognized as a hallmark of cancer and may represent a vulnerability to be exploited by targeted cancer therapy. Scientists from the research group of Giulio Superti-Furga, scientific director at the CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences and Professor at the Medical University of Vienna, have now used a drug library of 243 compounds targeting a variety of metabolic pathways to identify sensitivities among 15 myeloid leukemia cell lines. They were able to identify several specific pharmacological interventions possibilities."

This paper describes one of the latest new tools becoming available to combine enzyme engineering in the context of genome editing”

New gene-writing technology to develop more effective and safe therapies

by Universitat Pompeu Fabra – Barcelona, December 14, 2021

Maria Pallarès-Masmitjà et al, Find and cut-and-transfer (FiCAT) mammalian genome engineering, Nature Communications (2021). DOI: 10.1038/s41467-021-27183-x

Journal information: Nature Communications


". . . an efficient and precise programmable gene writing technology based on the combination of modified proteins CRISPR-cas and piggy Bac transposase (PB) for inserting small and large fragments. CRISPR stands out for its precision when editing small fragments. However, transposases allow us to insert large fragments but in an uncontrolled manner."


This paper reveals the advances in microscopy to view DNA at the nanometer scale and reduce impacts of diffraction distortion with current optical technology. The premise is that the dynamics and spacing of DNA wrapped up in nucleosomes within the Chromatin can better reveal the mechanisms of epigenetics.”

Live cell DNA arc hitecture in real time, by Elizabeth Hinde, Jieqiong Lou, Ashleigh Solano, Alex Hopper, University of Melbourne, December 14, 2021

Fluorescence lifetime imaging to study DNA compaction and gene activities


"Our work to date suggests chromatin architecture serves as a 'road map' for DNA-binding proteins to perform genome surveillance and localized DNA repair when damage arises."

This paper asks a very important question . . . Since human aging always ensures an accumulation of DNA mutations; "If we're simply looking for oncogenic mutations, we're always going to find them and they may not tell us much about cancer risk. How those oncogenic mutations are interfacing with the tissue environment will tell us so much more about risk.

Research demonstrates that cells with cancer-associated mutations overtake human tissue with age, by Rachel Sauer, CU Anschutz Medical Campus, December 13, 2021

Edward J. Evans et al, Cells with cancer‐associated mutations overtake our tissues as we age, Aging and Cancer (2021). DOI: 10.1002/aac2.12037


"Evans says future research could continue studying which oncogenic mutations are most likely to contribute to cancer and help to hone genetic screening tools to test for the most cancer-causing mutations.

"The vast majority of mutations don't do anything, they don't cause any problems, and many aren't even in coding sequences," DeGregori explains. "Every cell in our bodies has dozens and dozens of mutations, if not hundreds or thousands, so we have an opportunity to begin asking whether these patterns of mutations that we see can dictate whether someone is at high risk of cancer.""

This paper emphasizes the importance of understanding the Interactome and the changes in gene network dynamics. Just knowing about driver genes and their expressions is insufficient.

Gene Network changes associated with cancer onset and progression identify new candidates for targeted gene therapy by Georgia Institute of Technology, December 13, 2021

Zainab Arshad et al, Changes in gene-gene interactions associated with cancer onset and progression are largely independent of changes in gene expression, iScience (2021). DOI: 10.1016/j.isci.2021.103522

Journal information: iScience


In their latest study, McDonald and Bioinformatics Ph.D. student Zainab Arshad have found that another important class of genetic changes may be happening in places where scientists don't normally look: the network of gene-gene interactions associated with cancer onset and progression. "What I think is most remarkable about our findings is that the vast majority of changes—more than 90%—in the network of interactions accompanying cancer are not associated with genes displaying changes in their expression," adds Arshad, co-author of the paper. "What this means is that genes playing a central role in bringing about changes in network structure associated with cancer—the 'hub genes' [emphasis added]—may be important new targets for gene therapy that can go undetected by gene expression analyses."

When early-stage cancers develop, and stayed confined to their body tissue of origin, they noted a reduction in network complexity. as the cancers progress to advanced stages, when they can spread or metastasize to other parts of the body, "[W]e observe re-establishment of high levels of network complexity, but the genes comprising the complex networks associated with advanced cancers are quite different from those comprising the complex networks associated with the precursor normal tissues.... many of these changes are not detectable if all you're looking for are changes in gene expression." [emphasis added]

This paper raises the concern that there is more to the mystery of cancer than just a listing of mutations or drivers.

It's not all in their DNA: Cancer cells with the same genome can behave differently

by University of New South Wales, December 9, 2021

Katie A. Fennell et al, Non-genetic determinants of malignant clonal fitness at single-cell resolution, Nature (2021). DOI: 10.1038/s41586-021-04206-7

Journal information: Nature


"For the first time, research has shown cancer cells with the same genetic blueprint won't necessarily behave in the same way, with serious implications for how we target them. First author Dr. Katie Fennell says: "We developed a novel cellular barcoding technology that can track individual cancer cells (AML) over time and identify patterns that lead to different cell behavior—even when the underlying genome is the same." This barcoding technology (dubbed SPLINTR, which stands for Single-cell Profiling and LINeage TRacing) helps the researchers to identify the unique genes expressed in each leukemia cell, and monitor how this influences the cancer's behavior over time. They can then observe which acute myeloid leukemia cells are most likely to form cancerous tumors. This study highlights the importance of broadening the ambition of precision medicine beyond just surveying a patient's DNA mutations." [emphasis added]


"This is only one side of the coin. We urgently need to understand and develop treatments to also counter the non-genetic factors that influence cancer cell behavior," says Dr. Vassiliadis."

This paper reviews a possible target for personalized treatment - The puppet master: A chromatin remodeling complex called SWI/SNF, which controls the way in which DNA is arranged and compacted to fit within a cell's nucleus” While this study was done for Prostate cancer, It also suggests the possibility of using this approach for other types of cancer that are addicted to oncogenic transcription factors, including some multiple myelomas and other blood cancers.

Study demonstrates a novel approach to target enhancer-addicted cancers

by University of Michigan, December 27, 2021

Lanbo Xiao et al, Targeting SWI/SNF ATPases in enhancer-addicted prostate cancer, Nature (2021). DOI: 10.1038/s41586-021-04246-z

Journal information: Nature


"This is the first demonstration in cancer that blocking access to chromatin can be pursued as an avenue to treat cancer. They found that blocking the SWI/SNF complex slowed cancer cell growth and induced cell death. By disabling this SWI/SNF complex, we saw preferential activity against certain cancers and no toxicity in normal cells or normal tissues. This bodes well for clinical studies using compounds that target this pathway."



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