<?xml version="1.0" encoding="UTF-8"?><rss version="2.0"
	xmlns:content="http://purl.org/rss/1.0/modules/content/"
	xmlns:wfw="http://wellformedweb.org/CommentAPI/"
	xmlns:dc="http://purl.org/dc/elements/1.1/"
	xmlns:atom="http://www.w3.org/2005/Atom"
	xmlns:sy="http://purl.org/rss/1.0/modules/syndication/"
	xmlns:slash="http://purl.org/rss/1.0/modules/slash/"
	>

<channel>
	<title>CD20 &#8211; Science</title>
	<atom:link href="https://scienmag.com/tag/cd20/feed/" rel="self" type="application/rss+xml" />
	<link>https://scienmag.com</link>
	<description></description>
	<lastBuildDate>Wed, 14 Oct 2026 02:07:30 +0000</lastBuildDate>
	<language>en-US</language>
	<sy:updatePeriod>
	hourly	</sy:updatePeriod>
	<sy:updateFrequency>
	1	</sy:updateFrequency>
	<generator>https://wordpress.org/?v=7.1.3</generator>

<image>
	<url>https://scienmag.com/wp-content/uploads/2024/07/cropped-scienmag_ico-32x32.jpg</url>
	<title>CD20 &#8211; Science</title>
	<link>https://scienmag.com</link>
	<width>32</width>
	<height>32</height>
</image> 
<site xmlns="com-wordpress:feed-additions:1">73899611</site>	<item>
		<title>Enhanced CAR T-Cell Therapy Shows Promise in Trial for B-Cell Blood Cancers</title>
		<link>https://scienmag.com/enhanced-car-t-cell-therapy-shows-promise-in-trial-for-b-cell-blood-cancers/</link>
		
		<dc:creator><![CDATA[Nathaniel Bowman]]></dc:creator>
		<pubDate>Wed, 14 Oct 2026 02:07:30 +0000</pubDate>
				<category><![CDATA[Cancer]]></category>
		<category><![CDATA[B-cell blood cancers]]></category>
		<category><![CDATA[Blood Cancer Discovery]]></category>
		<category><![CDATA[CAR T-cell therapy for B-cell blood cancers]]></category>
		<category><![CDATA[CAR-T Cell Therapy]]></category>
		<category><![CDATA[CD19]]></category>
		<category><![CDATA[CD20]]></category>
		<category><![CDATA[CD22]]></category>
		<category><![CDATA[cell manufacturing]]></category>
		<category><![CDATA[chimeric antigen receptor T cell advancements]]></category>
		<category><![CDATA[clinical trial]]></category>
		<category><![CDATA[engineered T cells targeting multiple proteins]]></category>
		<category><![CDATA[first-in-human CAR T-cell study]]></category>
		<category><![CDATA[immune signaling enhancement in cancer therapy]]></category>
		<category><![CDATA[immune system amplification in cancer treatment]]></category>
		<category><![CDATA[Immunotherapy]]></category>
		<category><![CDATA[innovative cancer immunotherapy]]></category>
		<category><![CDATA[non-Hodgkin lymphoma]]></category>
		<category><![CDATA[Ohio State University]]></category>
		<category><![CDATA[Ohio State University cancer research]]></category>
		<category><![CDATA[OX40]]></category>
		<category><![CDATA[personalized cancer immunotherapy]]></category>
		<category><![CDATA[phase I clinical trial for relapsed B-cell cancers]]></category>
		<category><![CDATA[targeted immunotherapy for hematologic malignancies]]></category>
		<category><![CDATA[treatment-resistant blood cancer options]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=269663</guid>

					<description><![CDATA[A phase I trial at Ohio State found that CAR T cells engineered to target three B-cell proteins and boosted with OX40, manufactured in just six days and infused fresh, produced remissions with minimal side effects in patients with relapsed B-cell blood cancers.]]></description>
										<content:encoded><![CDATA[<p>A first-in-human clinical trial led by researchers at The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (OSUCCC – James) has reported encouraging results for an enhanced form of chimeric antigen receptor (CAR) T-cell therapy in patients with relapsed or treatment-resistant B-cell blood cancers. The phase I study, published in Blood Cancer Discovery, tested a cell product engineered to attack three different proteins found on malignant B cells while simultaneously deploying an additional signaling protein to amplify the immune attack. For a patient population that typically runs out of options after standard CAR T-cell therapy fails, the findings offer a potential path forward.</p>
<p>CAR T-cell therapy is one of the most significant advances in cancer medicine of the past decade. The process begins with the collection of T cells, the immune system&#8217;s primary cancer-killing soldiers, from a patient&#8217;s own blood. In the laboratory, those cells are genetically modified to express a chimeric antigen receptor, a synthetic molecule that allows the T cell to recognize a specific protein on the surface of cancer cells. Once infused back into the patient, the engineered cells multiply and launch a targeted assault on the tumor. The approach has produced high rates of remission in B-cell blood cancers, a category that accounts for roughly half of all blood cancers and includes lymphomas and certain leukemias.</p>
<p>Despite that success, a major weakness has limited the durability of the treatment. Many patients relapse after CAR T-cell therapy, often within the first year, leaving them with few remaining treatment options. One reason is that the therapy usually targets a single protein, CD19, which plays a central role in B-cell blood cancers. Cancer cells can survive the initial attack by losing or reducing expression of that single target, a phenomenon known as antigen escape. Building on earlier animal studies conducted at other institutions, the Ohio State team designed a therapy that targets three proteins at once: CD19, CD20 and CD22. By forcing the cancer to evade three distinct targets simultaneously, the trispecific construct is intended to make escape far more difficult.</p>
<p>The second innovation in the trial was the use of OX40, an immune costimulatory protein, to strengthen the activity of the engineered cells. According to Sumithira Vasu, MD, professor of hematology and a member of the Leukemia and Hematologic Malignancies Program at the OSUCCC – James, who served as the study&#8217;s first and corresponding author, this was the first time a CAR T-cell clinical trial used OX40 to enhance the process and improve tumor death. Costimulatory signals such as OX40 act like an accelerator for T cells, promoting their expansion, persistence and killing capacity after they encounter tumor cells. Vasu noted that results from the trial could lead to better therapeutic outcomes for patients who may have limited options after their B-cell blood cancer has returned or their therapy stopped working.</p>
<p>The trial also addressed a practical challenge that has long troubled the field: manufacturing time. Conventional CAR T-cell production can take weeks, during which aggressive cancers may progress and patients may deteriorate. The Ohio State team used a point-of-care manufacturing process that collected, prepared and returned the cells to the patient in just six days. Critically, the cells were infused fresh rather than frozen, a distinction that some researchers believe preserves the potency of the product. Lapo Alinari, MD, PhD, associate professor of hematology and lead senior co-author of the study, said it has been suggested that fresh cell infusions are preferable, and that the team was able to show the feasibility of rapid manufacturing time and infusion of fresh cells.</p>
<p>The clinical results supported that premise. Alinari reported that the rapid, fresh-cell approach produced meaningful clinical activity with minimal side effects in patients with B-cell non-Hodgkin lymphoma, and achieved remission in mantle cell lymphoma, follicular lymphoma and diffuse large B-cell lymphoma. These are distinct subtypes of B-cell malignancy with different biological behaviors, and achieving remissions across multiple subtypes suggests the trispecific strategy may have broad applicability. Equally important for an early-phase trial, the therapy was well tolerated, with patients experiencing minimal side effects, an encouraging safety signal for a technology that combines three tumor-targeting domains with an additional immune-boosting element.</p>
<p>Eighteen patients were enrolled in the study, with a median age of 64. Sixteen of them were treated with the OX40-enhanced CAR T-cell product. The patient population reflected the difficult reality of relapsed disease: all enrolled patients had previously received a median of three different types of therapy before receiving the enhanced cell therapy. In other words, these were heavily pretreated individuals whose cancers had already resisted multiple standard approaches, the very group in which new therapies are hardest to evaluate and for whom the unmet need is greatest.</p>
<p>The study was published in Blood Cancer Discovery, a peer-reviewed journal of the American Association for Cancer Research, with the article titled Safety and Clinical Outcomes of a First-in-Human Trial of Point-of-Care Manufactured Trispecific CAR T Cells Targeting CD19, CD20, and CD22. The research involved a broad team of investigators from Ohio State and Nationwide Children&#8217;s Hospital, reflecting the multidisciplinary effort required to move an engineered cell therapy from the laboratory bench to the bedside, including cell processing specialists, biostatisticians, and clinicians across hematology and oncology.</p>
<p>Senior co-author Marcos de Lima, MD, professor of hematology at Ohio State, cautioned that while the trial showed encouraging outcomes for patients with B-cell non-Hodgkin lymphoma treated with the enhanced CAR T-cells, more research in larger patient groups is needed. That caveat is standard and appropriate for a phase I study, which is primarily designed to establish safety and feasibility rather than to definitively measure efficacy. Larger trials will be required to confirm the remission rates, characterize the side-effect profile more completely, and determine whether the OX40 enhancement and trispecific targeting translate into longer-lasting remissions than current single-target products.</p>
<p>Nevertheless, the trial represents a notable step in the evolution of cellular immunotherapy. It combines three strategies that researchers have pursued independently, multi-antigen targeting to prevent immune escape, costimulatory enhancement to strengthen T-cell function, and rapid point-of-care manufacturing to deliver fresh cells before the disease can progress, into a single therapeutic platform. If subsequent studies validate these early findings, the approach could expand the reach of CAR T-cell therapy to patients who currently relapse after standard treatment, and the six-day manufacturing timeline could make this sophisticated form of personalized medicine faster and more accessible for the patients who need it most urgently.</p>
<p><strong>Subject of Research:</strong> A first-in-human phase I trial of trispecific OX40-enhanced CAR T-cell therapy for relapsed B-cell blood cancers</p>
<p><strong>Article Title:</strong> Clinical trial shows positive results of enhanced CAR T-cell therapy for patients with B-cell blood cancers</p>
<p><strong>Article References:</strong> Clinical trial shows positive results of enhanced CAR T-cell therapy for patients with B-cell blood cancers. (n.d.). <a href="https://www.eurekalert.org/news-releases/1147595" rel="noopener noreferrer">Original publication</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> Not provided</p>
<p><strong>Keywords:</strong> CAR T-cell therapy, B-cell blood cancers, non-Hodgkin lymphoma, CD19, CD20, CD22, OX40, clinical trial, immunotherapy, cell manufacturing, Ohio State University, Blood Cancer Discovery</p>
]]></content:encoded>
					
		
		
		<post-id xmlns="com-wordpress:feed-additions:1">269663</post-id>	</item>
		<item>
		<title>Global AI protein design contest puts 12,000 computer-made cancer binders to the test in living T cells</title>
		<link>https://scienmag.com/global-ai-protein-design-contest-puts-12000-computer-made-cancer-binders-to-the-test-in-living-t-cells/</link>
		
		<dc:creator><![CDATA[Nathaniel Bowman]]></dc:creator>
		<pubDate>Thu, 08 Oct 2026 20:51:52 +0000</pubDate>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[AI vs biological efficacy in cancer treatment]]></category>
		<category><![CDATA[AI-driven protein design]]></category>
		<category><![CDATA[antibody-like protein binders]]></category>
		<category><![CDATA[Artificial Intelligence]]></category>
		<category><![CDATA[artificial minibinders]]></category>
		<category><![CDATA[benchmarking]]></category>
		<category><![CDATA[cancer immunotherapy]]></category>
		<category><![CDATA[CAR T cells]]></category>
		<category><![CDATA[CD20]]></category>
		<category><![CDATA[challenges in translating computer-designed proteins to cellular environments]]></category>
		<category><![CDATA[chimeric antigen receptor (CAR) T cells]]></category>
		<category><![CDATA[de novo binders]]></category>
		<category><![CDATA[evaluation of AI-designed proteins in primary human T cells]]></category>
		<category><![CDATA[functional testing of designed proteins in living cells]]></category>
		<category><![CDATA[Immunotherapy]]></category>
		<category><![CDATA[open global competition in protein engineering]]></category>
		<category><![CDATA[pooled screening]]></category>
		<category><![CDATA[protein design]]></category>
		<category><![CDATA[Protein Engineering]]></category>
		<category><![CDATA[protein engineering for targeted cancer therapy]]></category>
		<category><![CDATA[protein-target interaction validation]]></category>
		<category><![CDATA[ProteinMPNN]]></category>
		<category><![CDATA[RFdiffusion]]></category>
		<category><![CDATA[translational stalling]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=249345</guid>

					<description><![CDATA[A global competition benchmarked 12,000 AI-designed CD20 binders in primary human CAR-T cells, revealing common design failure modes and simple filters that nearly doubled the rate of functional designs.]]></description>
										<content:encoded><![CDATA[<p>Artificial intelligence has become remarkably good at dreaming up proteins that stick to chosen targets, but a striking question has lingered behind the field&#8217;s headline successes: does a protein that binds on a computer actually work inside a living cell? A massive open competition called Bits to Binders has now delivered one of the most direct answers yet. Twenty-eight teams from 42 countries submitted 12,000 artificially designed minibinders, each exactly 80 amino acids long, intended to recognize the lymphoma surface antigen CD20 when deployed as the recognition domain of a chimeric antigen receptor, or CAR, in human T cells. Rather than scoring the designs by binding affinity alone, the organizers pushed every single one through a functional pipeline in primary human T cells, measuring whether the engineered cells proliferated, expanded, released cytokines, and killed tumor cells. The results, published in Molecular Systems Biology, reveal both the promise and the hidden failure modes of current AI protein design.</p>
<p>The competition&#8217;s premise deliberately raised the bar beyond standard binder benchmarks. A CAR binding domain must do far more than dock onto its antigen: it must be synthesized as DNA, expressed on the T cell surface within a fixed receptor scaffold, and trigger signaling that is strong enough to activate the cell but not so strong that the T cell becomes exhausted. Teams were told their 80-amino-acid binders would replace the single-chain variable fragment, or scFv, of a second-generation CAR28z construct, a domain that in natural antibodies typically runs 230 to 260 amino acids. Success ultimately depended on CAR-T cell function, not just molecular stickiness. Organizers provided primers on CAR-T biology, the exact scaffold, and assay details, then let competitors loose with whatever AI-driven workflows they preferred, creating an unusually diverse and honest snapshot of how the field actually designs proteins today.</p>
<p>The methodological landscape that emerged was dominated by generative diffusion models. Eighteen teams used RFdiffusion, two used sequence-structure co-design tools such as Chroma, and others turned to hallucination-based approaches like BindCraft, EvoBind, and ColabDesign, or protein language models including PepMLM, ESM-2, and RayGun. Nearly twenty teams employed ProteinMPNN or its soluble variant to design sequences onto fixed backbones, and seventeen used AlphaFold2 to verify that their creations were predicted to fold as intended. Twelve teams essentially followed the default RFdiffusion-ProteinMPNN-AlphaFold2 pipeline, while nine practiced iterative diffusion, trimming low-scoring segments and regenerating until scores improved. The result was extraordinary sequence diversity: more than 83 percent of submissions showed no significant alignment to any sequence from another team, although within-team redundancy was high, with a fifth of sequences nearly identical to a teammate&#8217;s design.</p>
<p>Testing 12,000 designs individually would have been impractical, so the organizers built a pooled screening system with elegant internal bookkeeping. Each codon-optimized binder sequence was cloned into the CAR plasmid library, where the binder itself served as a unique DNA barcode. Using the GeneWeld targeted integration method, the library was knocked into the T cell receptor alpha chain locus of primary human T cells, generating a pool of TRAC-negative, CAR-positive cells. After methotrexate selection using a co-expressed DHFR variant, the cells were split: one arm cultured alone, the other challenged repeatedly with mitotically inactivated CD20-positive Raji tumor cells. Over two weeks, binders that enabled productive antigen recognition drove proliferation of their host cells, and next-generation sequencing of the barcode region revealed which designs expanded. Comparing tumor-challenged cultures against the no-target controls allowed antigen-dependent growth to be quantified robustly for every design simultaneously.</p>
<p>The screen produced a sobering attrition curve. Nearly 98 percent of designs passed DNA synthesis quality control, but only 56.8 percent were recovered at sufficient sequencing depth after growth, implying that many binders failed to yield a viable CAR, likely because of poor expression, folding, or membrane localization. Ultimately, 707 designs, just under 6 percent, showed significant CD20-specific enrichment of at least twofold. Hit rates varied dramatically between teams, from 0.6 percent to 38.4 percent, a spread that itself encodes lessons about which strategies work. The ten best non-redundant designs advanced to individual validation, where each was rebuilt as a standalone CAR construct and subjected to a full battery of functional assays against CD20-positive Raji cells and CD20-negative K562 controls.</p>
<p>Seven of the ten leading designs outperformed untransfected control T cells in proliferation, expansion, and cytokine production, with flow cytometry confirming CAR expression in most of them. Designs 1506, 5300, and 5981 were the strongest cytokine producers, generating as much interleukin-2 and interferon-gamma as the scFv positive control, and design 5300 exceeded it. When it came to the most demanding readout, specific killing of CD20-positive targets, only four designs, 1506, 2383, 3494, and 3718, achieved significant target-specific lysis above background, and two of those matched the scFv control in specificity. Notably, several broadly functional designs showed no measurable binding in isolation, suggesting they may have relied on avidity or multivalent mechanisms within the receptor context. The pooled hit rate of 707 thus appears to be an upper bound on true functional success.</p>
<p>Surface plasmon resonance against detergent-solubilized CD20 added a crucial biophysical dimension. The scFv control bound with a dissociation constant of 1.75 nanomolar, but only three of the top ten designs showed appreciable binding: design 2383 at 643 nanomolar, and designs 1506 and 5981 with weak but detectable signals between roughly 200 and 600 nanomolar. The authors caution that this apparent preference for moderate or weak affinity is consistent with CAR biology, where excessively tight binding can drive trogocytosis and T cell exhaustion, and lower-affinity receptors have sometimes eliminated tumors better. However, the binding assay tested isolated 80-mers produced by bacterial cell-free synthesis rather than full receptors in mammalian cells, so some failures may reflect structural context rather than design quality. The team recommends that future efforts fold candidate binders within the complete CAR sequence, a computationally trivial step that only one team actually performed, and that team produced the top-performing design.</p>
<p>The most consequential findings came from mining the entire dataset for predictors of success and failure. The organizers computed more than 400 features per sequence, from GC content and Shannon entropy to predicted secondary structure and interface energies. Strikingly, 98.9 percent of designs that vanished from the proliferation screen had been created with ProteinMPNN or SolubleMPNN, and the failed designs were almost pure alpha helices, averaging 83 percent helical content, densely packed with lysine and glutamate. The ratio of residues in lysine-plus-glutamate helices was by far the strongest predictor of recovery failure, reaching 0.91 ROC-AUC in a cross-validated logistic model, averaging 35 percent of residues in failed designs versus 15 percent in recovered ones. The likely mechanism is translational interference: glutamate repeats are known to stall ribosomes, and lysine and glutamate codons produce adenosine-rich DNA, with poly-A tracks also disrupting translation. Failed sequences carried nearly four glutamate-glutamate repeats on average versus 1.6 in recovered designs, and adenosine dinucleotide repeats predicted recovery with 0.88 ROC-AUC. An independent phage display study has since confirmed the lysine-glutamate association, suggesting the signal generalizes well beyond CAR-T cells.</p>
<p>Other failure modes emerged with equal clarity. Designs that caused CD20-specific depletion of T cells, possibly reflecting exhaustion, were enriched in cysteines predicted to form intramolecular disulfide bonds, which may have exposed hinge sulfhydryls and amplified tonic signaling. DNA synthesis failures clustered among sequences with high GC content and low entropy. Perhaps most humbling for the structure-prediction community, the standard confidence metrics, including ipTM, pLDDT, ipSAE, LIS, SAP, PDockQ, and language-model likelihoods, showed little predictive power for functional outcomes, and most teams&#8217; own confidence rankings correlated poorly, or even negatively, with experimental success. Simple sequence statistics beat sophisticated structure-based scores. Applying retrospective filters for GC content, entropy, adenosine repeats, glutamate repeats, and lysine-glutamate helix content removed 4,600 sequences and nearly doubled the proportion of designs showing CD20-specific proliferation, from 5.9 to 7.6 percent, rising to 10.6 percent with a cysteine filter that would also have eliminated two of the non-functional top-ten designs.</p>
<p>The authors are careful about the study&#8217;s limits: a single CAR scaffold, a single donor isolate, a comparison of Raji-challenged cells against no-target rather than CD20-negative controls, and a design space constrained to 80 amino acids all shape the conclusions. No design is remotely clinic-ready, and all underperformed the scFv control in most readouts. Yet the significance of the work lies less in any single binder than in the demonstration that generative protein design can now be evaluated end-to-end in a therapeutic context, at scale, in the open. The dataset has been released on Zenodo with code on GitHub, and the practical recommendations, avoid lysine-glutamate helix overload, watch for cysteines, fold within the full receptor, and treat moderate affinity as a feature rather than a bug, offer the field its first empirically grounded playbook for designing proteins that do not merely bind, but function inside living cells.</p>
<p><strong>Subject of Research:</strong> Experimental validation of AI-designed de novo protein binders as CAR-T cell recognition domains targeting CD20</p>
<p><strong>Article Title:</strong> Validation and analysis of 12,000 AI-driven CAR-T designs in the Bits to Binders competition</p>
<p><strong>Article References:</strong> Kosonocky, C. W., Abel, A. M., Feller, A. L., Cifuentes Rieffer, A. E., Woolley, P. R., Lála, J., Barth, D. R., Gardner, T., Bits to Binders Competitors, Acosta, D., Angioletti-Uberti, S., Annapure, V., Anthony, N., Barghout, R. A., Beining, M., Bibekar, P., Biton, D., Bryant, P., Bushuiev, A., &#8230; Marcotte, E. M. (2026). Validation and analysis of 12,000 AI-driven CAR-T designs in the Bits to Binders competition. <em>Molecular Systems Biology</em>. <a href="https://doi.org/10.1038/s44320-026-00246-1" rel="noopener noreferrer">https://doi.org/10.1038/s44320-026-00246-1</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1038/s44320-026-00246-1" rel="noopener noreferrer">10.1038/s44320-026-00246-1</a></p>
<p><strong>Keywords:</strong> CAR-T cells, protein design, artificial intelligence, CD20, ProteinMPNN, RFdiffusion, de novo binders, pooled screening, protein engineering, immunotherapy, translational stalling, benchmarking</p>
]]></content:encoded>
					
		
		
		<post-id xmlns="com-wordpress:feed-additions:1">249345</post-id>	</item>
		<item>
		<title>AI-Designed Protein Binders Face Real-World Test in Landmark CAR T Cell Competition</title>
		<link>https://scienmag.com/ai-designed-protein-binders-face-real-world-test-in-landmark-car-t-cell-competition/</link>
		
		<dc:creator><![CDATA[Drew Townsend]]></dc:creator>
		<pubDate>Thu, 08 Oct 2026 12:51:24 +0000</pubDate>
				<category><![CDATA[Biology]]></category>
		<category><![CDATA[AI-designed protein binders]]></category>
		<category><![CDATA[AlphaFold2 breakthrough]]></category>
		<category><![CDATA[artificial intelligence in biology]]></category>
		<category><![CDATA[benchmarking]]></category>
		<category><![CDATA[Bits to Binders]]></category>
		<category><![CDATA[CAR T cells]]></category>
		<category><![CDATA[CAR-T Cell Therapy]]></category>
		<category><![CDATA[CASP]]></category>
		<category><![CDATA[CASP protein structure prediction]]></category>
		<category><![CDATA[CD20]]></category>
		<category><![CDATA[computational biology]]></category>
		<category><![CDATA[generative AI]]></category>
		<category><![CDATA[genomics and therapeutic discovery]]></category>
		<category><![CDATA[Immunotherapy]]></category>
		<category><![CDATA[large-scale protein design competition]]></category>
		<category><![CDATA[minibinders]]></category>
		<category><![CDATA[Molecular Systems Biology]]></category>
		<category><![CDATA[open competition in protein design]]></category>
		<category><![CDATA[prospective assessment of AI methods]]></category>
		<category><![CDATA[protein design]]></category>
		<category><![CDATA[Protein Engineering]]></category>
		<category><![CDATA[protein engineering for immunotherapy]]></category>
		<category><![CDATA[protein recognition domain development]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=247782</guid>

					<description><![CDATA[A crowdsourced competition called Bits to Binders tested 12,000 AI-designed minibinders as CAR T cell recognition domains, revealing both the promise and the pitfalls of generative protein design for cancer immunotherapy.]]></description>
										<content:encoded><![CDATA[<p>More than three decades ago, structural biologists created the Critical Assessment of Structure Prediction, or CASP, to rigorously evaluate methods for predicting protein structures from amino acid sequences. Participants submitted predictions before the corresponding experimental structures became publicly available, establishing a common standard against which methodological advances could be measured. The value of that framework became unmistakable at CASP14 in 2020, when AlphaFold2 produced predictions approaching experimental accuracy for many targets. Independent, prospective assessment allowed the scientific community to grasp the scale of the breakthrough almost immediately, because the results could not be explained by hindsight or selective reporting. According to a News and Views commentary published in Molecular Systems Biology by Abdul Vehab Dozic and Caleb A Lareau of Memorial Sloan Kettering Cancer Center, the next generation of CASP-like open competitions is now poised to do the same for emerging artificial intelligence methods across biology, from genomics to protein design to therapeutic discovery.</p>
<p>One such effort, described in the same issue of the journal, is the Bits to Binders competition, in which Kosonocky, Abel and colleagues evaluated roughly 12,000 designed proteins as recognition domains for chimeric antigen receptor, or CAR, T cells. The scale of the undertaking is remarkable: twenty-eight teams submitted designs generated using diverse computational workflows, and each design was inserted into a common CAR scaffold for evaluation in primary human T cells. This design choice matters enormously, because it isolates the variable of interest, the binder itself, from the many other components that determine whether a cell therapy works. By holding the scaffold constant, the organizers could ask a deceptively simple question with profound implications: which AI-generated proteins can actually redirect a living immune cell to kill a cancer cell?</p>
<p>The molecular players at the center of the competition are minibinders, highly compact proteins that generative AI methods produce with increasing reliability. Unlike the antibody-derived single-chain variable fragments, or scFvs, conventionally used for antigen recognition in CAR T cells, minibinders typically comprise alpha helices and beta sheets arranged in small structures of roughly 65 to 80 amino acids, with well-folded architectures and programmable binding interfaces. While antibodies have historically been the dominant format for therapeutic protein binders, minibinders have already demonstrated heterogeneous uses in the academic literature, ranging from biosensors to viral neutralization, including picomolar inhibitors of SARS-CoV-2 designed de novo, to recognition domains in cell therapies targeting antigens in glioblastoma. Their ultimate therapeutic efficacy, however, has yet to be determined, which is precisely why a functional benchmark matters.</p>
<p>Earlier candidates from de novo protein design were largely assessed on biophysical parameters such as predicted stability, solubility, and affinity for a chosen target. Community competitions, including challenges supported by the company Adaptyv Bio, have begun to compare design workflows through standardized measurements of protein expression and binding affinity. But as the field moves toward repurposing these binders as therapeutic biologics, such criteria become necessary yet insufficient, because each therapeutic modality carries additional constraints. Extending the benchmarking framework to therapeutic applications requires tests that establish whether molecular recognition actually translates into the intended biological response. Bits to Binders was built to answer exactly that question, establishing an open community effort to assess the functional potential of AI-designed minibinders inside CAR T cells, the context in which they would ultimately need to perform.</p>
<p>The biological target chosen for the competition was CD20, a surface protein expressed by normal B cells and many B-cell malignancies. CARs work by repurposing antigen-binding domains to focus T cells toward specific target antigens on tumor cell surfaces, and the competition used the well-characterized antibody rituximab as a benchmark scFv alongside the de novo designs. Productive CAR function, however, demands far more than binding. A receptor must be expressed on the T cell surface, its binding epitope must be accessible on the target cell, and it must trigger appropriate signaling. Recent characterization of de novo CARs identified signaling without a target, inaccessible binding epitopes, and off-target activation as distinct constraints on efficacy that go well beyond simple binding, underscoring the importance of evaluating designed binders in their intended cellular context rather than in a test tube.</p>
<p>To capture these complexities at scale, the organizers used each binder-encoding sequence as a molecular barcode to track its corresponding CAR T cells in a pooled proliferation screen. After growth, 6,811 designs met the sequencing recovery threshold, and 707 of those showed significant enrichment in cultures containing CD20-positive lymphoma cells relative to cultures without them. The funnel then narrowed sharply. Individual testing of ten leading designs confirmed increased proliferation, expansion, and cytokine production for seven compared with unmodified T cells. Four showed significant selective killing in comparisons involving CD20-positive and CD20-negative cell lines. The designs generally underperformed the antibody-derived CAR control, indicating that further optimization remains necessary before AI-generated minibinders can match the refined binding domains that decades of antibody engineering have produced.</p>
<p>Perhaps the most sobering finding came from the biochemical side of the validation. Only three of the designs showed validated binding in biochemical assays, whose conditions differed from the cellular context of the proliferation screen. That disconnect between cell-based activity and cell-free binding measurements is itself an important result, because it suggests that computational predictions of affinity do not reliably predict function inside a living cell. Nevertheless, the retrospective analyses of sequences that failed at each step of the pipeline nominated concrete criteria for prospective testing, including screening DNA sequences for high GC content and repetitive elements, and limiting excessive enrichment of lysine and glutamate residues in helical structures. These are exactly the kind of actionable design rules that open competitions are uniquely positioned to generate, since no single laboratory could test such a diverse portfolio of approaches on its own.</p>
<p>The commentary authors are careful to note several caveats that signal opportunities to strengthen future competitions. The pooled screen assessed CAR behavior with or without lymphoma cells, but additional controls, such as isogenic knockout cell lines, would be needed to specifically tie activity to CD20 rather than to some other feature of the tumor cells. Testing a single receptor scaffold and a single T-cell donor also limits how far the sequence features identified in the binders can be generalized. Moreover, differences in the designed sequences reflect distinct workflows, including sequence selection and refinement steps, which makes it difficult to attribute performance to any individual algorithm. Future competitions that expand experimental validation and invite submissions annotated with the specific pipeline components being tested may better isolate the principles that separate efficacious therapeutic designs from expensive failures.</p>
<p>Looking forward, sustaining open competitions of this kind will require durable support for experimental testing, independent assessment, and shared data resources. The history of CASP offers a cautionary tale: despite decades of public funding, the competition faced lapses in support and secured a one-time private gift only in 2025 to keep running. As emerging competitions with more diverse endpoints, including Bits to Binders, expand the scope and promise of AI-enabled community benchmarking, they will similarly require sustained investment in the infrastructure necessary to realize biological breakthroughs. The stakes are considerable. If generative AI can reliably produce functional therapeutic binders, the design-build-test cycle for cell therapies could compress from years to months. Bits to Binders has now shown, with unusual transparency, both how far the technology has come and how much distance remains between a computationally elegant protein and a medicine that works in a patient.</p>
<p><strong>Subject of Research:</strong> Benchmarking AI-designed minibinders as functional recognition domains in CAR T cell therapy through an open competition</p>
<p><strong>Article Title:</strong> Crowdsourcing functional cell therapy binders from generative artificial intelligence</p>
<p><strong>Article References:</strong> Dozic, A. V., &amp; Lareau, C. A. (2026). Crowdsourcing functional cell therapy binders from generative artificial intelligence. <em>Molecular Systems Biology</em>. <a href="https://doi.org/10.1038/s44320-026-00249-y" rel="noopener noreferrer">https://doi.org/10.1038/s44320-026-00249-y</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1038/s44320-026-00249-y" rel="noopener noreferrer">10.1038/s44320-026-00249-y</a></p>
<p><strong>Keywords:</strong> generative AI, protein design, minibinders, CAR T cells, Bits to Binders, CASP, CD20, immunotherapy, protein engineering, benchmarking, Molecular Systems Biology, computational biology</p>
]]></content:encoded>
					
		
		
		<post-id xmlns="com-wordpress:feed-additions:1">247782</post-id>	</item>
		<item>
		<title>Immune Cell Clusters Inside Brain Tumors Predict Glioblastoma Survival</title>
		<link>https://scienmag.com/immune-cell-clusters-inside-brain-tumors-predict-glioblastoma-survival/</link>
		
		<dc:creator><![CDATA[Nathaniel Bowman]]></dc:creator>
		<pubDate>Sat, 03 Oct 2026 22:18:58 +0000</pubDate>
				<category><![CDATA[Cancer]]></category>
		<category><![CDATA[brain tumor immunology]]></category>
		<category><![CDATA[CD20]]></category>
		<category><![CDATA[CD3]]></category>
		<category><![CDATA[Cox regression]]></category>
		<category><![CDATA[Glioblastoma]]></category>
		<category><![CDATA[glioblastoma prognosis]]></category>
		<category><![CDATA[glioblastoma survival prediction]]></category>
		<category><![CDATA[IDH-wildtype]]></category>
		<category><![CDATA[immune cell clusters in glioblastoma]]></category>
		<category><![CDATA[immune cell organization in tumors]]></category>
		<category><![CDATA[immune infiltration in glioblastoma]]></category>
		<category><![CDATA[immune system role in brain cancer]]></category>
		<category><![CDATA[immune-based tumor stratification]]></category>
		<category><![CDATA[immunohistochemistry]]></category>
		<category><![CDATA[Immunotherapy]]></category>
		<category><![CDATA[neuro-oncology]]></category>
		<category><![CDATA[overall survival]]></category>
		<category><![CDATA[prognostic markers]]></category>
		<category><![CDATA[tertiary lymphoid structures]]></category>
		<category><![CDATA[tertiary lymphoid structures in brain tumors]]></category>
		<category><![CDATA[TLS as prognostic markers]]></category>
		<category><![CDATA[tumor immune microenvironment]]></category>
		<category><![CDATA[tumor microenvironment]]></category>
		<category><![CDATA[tumor microenvironment immune response]]></category>
		<guid isPermaLink="false">https://scienmag.com/?p=232266</guid>

					<description><![CDATA[A new grading system for tertiary lymphoid structures in glioblastoma tissue identifies patients with significantly longer survival and may guide immunotherapy selection.]]></description>
										<content:encoded><![CDATA[<p>Glioblastoma remains one of the most feared diagnoses in medicine, a brain tumor that resists surgery, radiation, and chemotherapy with brutal efficiency. Yet a new study suggests that the answer to predicting which patients will live longer may already be visible under the microscope, hidden in unexpected structures within the tumor itself. Researchers report that clusters of immune cells known as tertiary lymphoid structures, or TLS, can be graded in a way that sharply distinguishes patients with longer survival from those with shorter outcomes, offering a fresh prognostic lens on a disease that has stubbornly resisted every attempt at stratification.</p>
<p>Tertiary lymphoid structures are organized aggregates of immune cells that form outside the conventional lymph nodes and spleen. In many solid tumors, they are viewed as encouraging signs: evidence that the immune system has mounted a localized, sustained response against the malignancy. These structures typically contain T cells and B cells arranged in patterns that resemble miniature lymphoid organs, sometimes even developing the germinal centers where antibodies are refined. In cancers such as melanoma, lung cancer, and breast cancer, the presence and density of TLS have repeatedly been linked to better responses to immunotherapy and improved survival. The brain, however, has long been considered an immunologically quiet environment, protected by the blood-brain barrier and populated by its own specialized immune cells, so the role of TLS in brain tumors has remained far less clear.</p>
<p>That gap is precisely what a team of neurosurgeons and researchers affiliated with Kunming Medical University and collaborating institutions in China set out to address. In a retrospective study published in the journal Cancer Immunology, Immunotherapy, the investigators analyzed tissue samples from 62 patients with isocitrate dehydrogenase, or IDH, wildtype glioblastoma who were treated at their institution between 2016 and 2023. IDH wildtype status defines the most aggressive and common form of glioblastoma in adults, and it is the subtype for which new prognostic tools are most urgently needed. The study was conducted in accordance with the Declaration of Helsinki, with ethics approval from the First Affiliated Hospital of Kunming Medical University and written informed consent obtained from all participants or their legal representatives.</p>
<p>The methodological heart of the study lies in how the researchers detected and classified these immune structures. Using standard hematoxylin and eosin staining alongside immunohistochemical staining for CD3, a marker of T cells, and CD20, a marker of B cells, the team identified TLS within resected tumor specimens. Rather than simply recording whether TLS were present or absent, the investigators went a step further and built a grading system that captured two dimensions: the quantity of the structures and their spatial distribution within the tumor region. This distinction matters because a TLS sitting in the peritumoral zone, the tissue surrounding the tumor, may reflect a different immunological situation than one embedded deep within the tumor mass itself, where it would be in direct contact with malignant cells.</p>
<p>The results were striking. TLS were present in 58.1 percent of the cohort, meaning that more than half of these patients carried organized immune structures in or around their tumors. When the researchers correlated TLS status with overall survival using Kaplan-Meier curves, they found that TLS presence, TLS grading, and the extent of surgical resection all showed statistically significant associations with survival outcomes, each reaching the threshold of P less than 0.05. The grading system proved particularly informative. Patients with higher TLS grades, and especially those whose structures were located within the tumor itself, corresponding to the highest category, Score 3, experienced significantly prolonged overall survival compared with patients lacking these structures or harboring only peritumoral ones.</p>
<p>To ensure that this association was not simply a statistical artifact driven by other clinical variables, the team turned to multivariate Cox regression analysis, a standard statistical technique that evaluates the independent contribution of each factor while controlling for the others. The analysis confirmed that TLS grading stood as an independent favorable prognostic factor for overall survival in this glioblastoma cohort. In practical terms, this means that even after accounting for variables such as the extent of resection, the grade of the TLS carried its own predictive weight. The extent of resection, which distinguishes total, subtotal, and partial removal of the tumor, also remained significantly correlated with survival, consistent with decades of neurosurgical evidence, but the TLS signal held its ground alongside it.</p>
<p>The implications of these findings extend beyond prognosis into the realm of treatment selection. Glioblastoma has been a notoriously poor responder to immune checkpoint inhibitors, the class of drugs that has revolutionized the treatment of many other cancers. One leading explanation is that the brain tumor microenvironment lacks the pre-existing immune infrastructure that such therapies require to work. TLS could represent exactly that infrastructure: a localized factory for generating and deploying tumor-specific immune cells. If patients whose tumors contain high-grade, intratumoral TLS are the ones with an already-primed immune response, they may be the subset most likely to benefit from intensified immunotherapeutic interventions, while patients without TLS might need strategies that first induce lymphoid neogenesis before checkpoint blockade could have any chance of success.</p>
<p>The authors are appropriately measured in their claims. They emphasize that the proposed TLS grading system provides a potential prognostic stratification tool for glioblastoma that warrants external validation, a crucial caveat in a field where promising single-institution findings sometimes fail to replicate in larger, independent cohorts. With 62 patients, the study is a meaningful proof of concept but not a definitive clinical standard. Standardizing how TLS are identified and scored across pathology laboratories, and testing the grading system in independent datasets from other centers, will be essential steps before it could inform treatment decisions at the bedside. The retrospective design also means that the findings demonstrate association rather than causation, and it remains possible that TLS are a marker of some other underlying biological difference rather than an active driver of better outcomes.</p>
<p>Even with those caveats, the study adds an important piece to the evolving picture of glioblastoma immunology. The tumor microenvironment, once viewed as a hostile wasteland for immune activity, is increasingly understood as a complex ecosystem where organized immune structures can and do form. The fact that the location of these structures, not just their number, carries prognostic weight suggests that the spatial architecture of the anti-tumor immune response matters, a principle that resonates with broader trends in cancer immunology where spatial biology is reshaping how tumors are classified. For a disease in which median survival has barely moved in decades, any new, independently validated prognostic factor is significant, and one that could also guide immunotherapy selection would be doubly valuable.</p>
<p>The research, published as an open-access article, was supported by funding from Kunming Medical University, the Health Commission of Yunnan Province, and related regional research programs. The authors reported no relevant financial or non-financial conflicts of interest. As the field moves forward, the challenge will be to translate this grading system from the research laboratory into routine pathology workflows, where hematoxylin and eosin slides and CD3 and CD20 stains are already standard tools. If external validation confirms what this cohort suggests, neuro-oncologists may one day look at a glioblastoma specimen not only for the features that define its malignancy, but for the quiet architecture of the immune response unfolding within it, and use that architecture to decide which patients need the most aggressive immunological reinforcements available.</p>
<p><strong>Subject of Research:</strong> Tertiary lymphoid structures as prognostic biomarkers in IDH-wildtype glioblastoma</p>
<p><strong>Article Title:</strong> Tertiary lymphoid structures (TLS) classification: a new perspective on glioblastoma patient’s prognosis</p>
<p><strong>Article References:</strong> Meng, M., Li, Y., Dai, X., Yang, G., Li, Z., &amp; Tang, Z. (2026). Tertiary lymphoid structures (TLS) classification: a new perspective on glioblastoma patient’s prognosis. <em>Cancer Immunology, Immunotherapy</em>. <a href="https://doi.org/10.1007/s00262-026-04537-2" rel="noopener noreferrer">https://doi.org/10.1007/s00262-026-04537-2</a></p>
<p><strong>Image Credits:</strong> AI Generated</p>
<p><strong>DOI:</strong> <a href="https://doi.org/10.1007/s00262-026-04537-2" rel="noopener noreferrer">10.1007/s00262-026-04537-2</a></p>
<p><strong>Keywords:</strong> glioblastoma, tertiary lymphoid structures, tumor microenvironment, prognostic markers, immunotherapy, IDH-wildtype, immunohistochemistry, overall survival, neuro-oncology, Cox regression, CD3, CD20</p>
]]></content:encoded>
					
		
		
		<post-id xmlns="com-wordpress:feed-additions:1">232266</post-id>	</item>
	</channel>
</rss>
