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New Single‑Cell Platform Tracks RNA and Protein in Immune Signaling

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A new single‑cell sequencing method is giving researchers a clearer view of how immune cells actually behave—capturing not just what they plan to do, but what they are doing in real time. The platform, called CIPHER‑seq, measures RNA and proteins simultaneously inside the same immune cell, exposing gaps between genetic intent and functional output that have long complicated studies of cytokine signaling. The work, titled “CIPHER-seq enables intracellular multimodal profiling of cytokine responses in single immune cells,” appears in Scientific Reports.

Single‑cell RNA sequencing has reshaped immunology by revealing which genes are switched on across thousands of cells at once. But RNA alone can be misleading, especially for cytokines. However, RNA is only a set of instructions; proteins carry out the action. And for cytokines, RNA levels often fail to predict how much protein a cell actually produces. “In immune cells, RNA and protein don’t always rise and fall together,” said co‑senior author Emiliano Cocco, PhD, an assistant professor of biochemistry and molecular biology at the Miller School.

CIPHER‑seq (Cytokine Intracellular Protein High-throughput Expression with RNA-sequencing) was designed to close that gap. Developed by researchers at the Sylvester Comprehensive Cancer Center at the University of Miami Miller School of Medicine, together with collaborators at UCSF and the Helen Diller Family Comprehensive Cancer Center, the method gently preserves cells and captures multiple molecular layers at once. From a single immune cell, CIPHER‑seq can quantify genome‑wide RNA, surface proteins, intracellular proteins, and cytokines that have not yet been released—creating a more complete snapshot of immune activity than RNA‑only approaches.

“RNA gives us clues about where a cell is headed,” said co‑senior author Justin Taylor, MD, a Sylvester physician-scientist. “Proteins show us where it actually arrives, and this clearer picture could help scientists design better immunotherapies and help clinicians predict which patients are most likely to benefit from them.”

The team validated the platform by stimulating peripheral blood mononuclear cells (PMBCs) and tracking their responses. According to the study, CIPHER‑seq captured robust induction of key cytokines—including interferon‑gamma and tumor necrosis factor—while also resolving metabolic remodeling during activation. Importantly, the method revealed the timing of these events: RNA signals rose first, followed by delayed but consistent protein accumulation. First author Avni Bhalgat, PhD, described it as “seeing the plan before the action. Cytokines help determine whether immune cells attack cancer, ignore it, or even help tumors grow.”

The researchers also compared CIPHER‑seq with standard single‑cell workflows and found a notable difference: cells processed with CIPHER‑seq showed far fewer mitochondrial stress signatures. Some existing protocols inadvertently damage cells during preparation, triggering artificial stress responses. By reducing these artifacts, CIPHER‑seq provides a cleaner readout of immune behavior.

The authors emphasize that this multimodal view is especially valuable for studying cancer, inflammation, and treatment resistance—contexts where cytokine timing and protein abundance can shape therapeutic outcomes. “The platform helps us move beyond inference and toward understanding how immune responses truly unfold—one cell at a time,” Taylor added. By tracking RNA and protein together, CIPHER‑seq moves researchers beyond inference and toward a step‑by‑step understanding of how immune responses unfold.

The post New Single‑Cell Platform Tracks RNA and Protein in Immune Signaling appeared first on GEN – Genetic Engineering and Biotechnology News.

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STAT+: At hospital finance conference, a call to end the friction that’s keeping costs high

NATIONAL HARBOR, Md. — At this week’s annual meeting of hospital finance leaders, the exhibit hall was packed with dozens of billing and collections companies. Armed with candy, tote bags, and pens, they smiled at passersby, eager to explain why their tactics would extract the most money from health insurers. 

The sheer number of “revenue cycle” vendors who attended the Healthcare Financial Management Association’s annual conference in Maryland — outnumbering even the hospital attendees, according to a list shared by an organizer — was a visible reminder of the enormous industry built around just paying medical bills. 

The U.S. health care industry spends roughly $200 billion annually on financial transactions: claims processing, payment, collections, and prior authorization. And yet the proliferation of billing vendors seemed to clash with the main theme of HFMA’s conference, affordability, spotlighting the need to simplify the billing process so that health care is less costly and more accessible for patients. 

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NATIONAL HARBOR, Md. — At this week’s annual meeting of hospital finance leaders, the exhibit hall was packed with dozens of billing and collections companies. Armed with candy, tote bags, and pens, they smiled at passersby, eager to explain why their tactics would extract the most money from health insurers. 

The sheer number of “revenue cycle” vendors who attended the Healthcare Financial Management Association’s annual conference in Maryland — outnumbering even the hospital attendees, according to a list shared by an organizer — was a visible reminder of the enormous industry built around just paying medical bills. 

The U.S. health care industry spends roughly $200 billion annually on financial transactions: claims processing, payment, collections, and prior authorization. And yet the proliferation of billing vendors seemed to clash with the main theme of HFMA’s conference, affordability, spotlighting the need to simplify the billing process so that health care is less costly and more accessible for patients. 

Continue to STAT+ to read the full story…

Read More

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Beyond sunshine: Iberia’s biotech moment has arrived with developing capital networks

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Strong science, lower costs and growing capital networks are putting Spain and Portugal on the biotech investment map, even as structural bottlenecks persist, according to two investors.

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Laser‑Driven Phase Contrast Enhances Cryo‑EM Resolution of Small Proteins

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You know when you are at the eye doctor getting an updated prescription, and suddenly the world snaps into sharper focus? Physicists at the University of California (UC), Berkeley, have now done something similar for electron microscopy. By introducing phase contrast into a cryo‑electron microscope, they have delivered dramatically sharper images of some of biology’s smallest and most elusive proteins.

The advance comes from a new laser phase plate (LPP), described in the paper “Laser phase plate improves structure determination of small proteins by cryo‑EM,” which was published recently in Science. Led by physicist Holger Mueller, PhD, of UC Berkeley and Lawrence Berkeley National Laboratory, the team demonstrated that a laser‑driven phase plate can overcome one of cryo‑EM’s most persistent limitations: poor contrast for small proteins.

Cryo-EM images of two proteins, apoferritin and hemoglobin, taken without and with a laser phase plate. The images are analyzed in a computer to produce detailed 3D structures of the proteins. [Holger Müller, Jessie Zhang/UC Berkeley]

Cryo‑EM has transformed structural biology over the past decade, earning a Nobel Prize in 2017 for enabling high‑resolution structures without crystallization. But despite its impact, the technique still struggles with proteins below ~70 kilodaltons—a size range that includes about 90% of the human proteome. “Because of signal-to-noise limitations, the majority of human and animal proteins are too small to be analyzed by these methods [cryo-EM and cryoelectron tomography]. The increase in signal-to-noise ratio provided by this laser phase plate is expected to overcome these important limitations.”

The new LPP begins to address that problem. The LPP uses an intense, continuous‑wave laser to shift the phase of the electron beam itself. This produces true phase contrast without dimming or destabilizing the beam. Mueller described the laser focus as “75 kilowatts focused to a few microns… That’s more powerful than what you use for welding. It has more power than a military laser. It builds up the brightest continuous laser focus ever.”

Installed in a custom Thermo Fisher Titan Krios, the LPP immediately improved the clarity and resolvability of small proteins, including hemoglobin, which sits at the lower limit of what today’s cryo‑EM instruments can handle. As the authors wrote in the abstract: “Here, we show that the laser phase plate (LPP)… enhances the resolution in single-particle reconstruction of small proteins by improving specimen-motion correction, recovery of information from the early frames, as well as particle visualization, 3D classification, and alignment.”

phase plate cover Cryo-EM
A laser (purple) is powerfully amplified by highly polished mirrors and focused on the electron beam (blue) to shift its phase and increase the cryo-EM microscope’s contrast, allowing biologists to image smaller proteins and the crowded structures inside cells. [Sayo Studio]

These improvements were achieved using standard defocus ranges and reconstruction workflows. “For the most challenging cases—small particles, bad specimens—the laser produces a very considerable advantage,” Mueller said.

 

The impact extends beyond single‑particle analysis. Cryo‑electron tomography (cryo‑ET), which assembles multiple angular views of a molecule or protein into a three-dimensional image, stands to benefit even more. “With cryo-ET, we’re looking at small, very complicated cellular material that’s incredibly crowded inside the cell,” said Bridget Carragher, PhD, founding technical director of imaging at Biohub. “It’s like a forest of trees, and you’re trying to find one leaf on one tree in there. Cryo-ET needs a dramatic step forward in contrast, so we can start to see what’s going on inside the cell. That’s what the laser phase plate promises to give us.”

Biohub is developing a dual‑laser version of the system, designed to reduce component wear and minimize aberrations. Meanwhile, Mueller’s team is pushing toward imaging proteins as small as 17 kilodaltons, a threshold that would open access to vast regions of the human proteome previously invisible to cryo‑EM.

“This technology is a step function change for biology,” said Stephani Otte, PhD, Biohub’s vice president of imaging science. “What was once invisible will become visible—and that changes everything about how we understand disease.”

“The bottom line is, if you have a large protein and a really good sample—a fresh one or one frozen without bubbles, for example—you may not need the phase plate to get a single, high-quality image. But for a small protein and a bad sample, laser-on is best,” Mueller said. “This could fill an enormous gap in our knowledge of protein structures that can’t be crystallized or are too small for today’s cryo-EM. And it will be revolutionary for cryo-ET.”

The post Laser‑Driven Phase Contrast Enhances Cryo‑EM Resolution of Small Proteins appeared first on GEN – Genetic Engineering and Biotechnology News.

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