godfather of surgery

Chapter 1305 New Discovery
The three shut down the equipment and left the laboratory, leaving the corridor silent.

As Griffin reached the top of the stairs, he suddenly stopped. "Dr. Zhang, thank you."

"no need thank me?"

“You reminded us that when studying structures, we can’t just look at the shape; we also have to think about how it works. That observation of the charge distribution could save us weeks of time.”

Zhang Lin was a little embarrassed: "I was just guessing... But the professor often says that scientific research requires both rigorous data and bold imagination, and neither can be lacking. I only have a little unreliable imagination."

“Professor Yang is right.” Griffin nodded seriously.

The three walked toward the duty room, where the laboratory had many duty rooms for people to take a nap at noon and stay overnight temporarily.

The next morning, Yang Ping was reviewing the preliminary structural analysis report submitted by Lu Xiaolu in his office when Griffin knocked on the door and came in.

“Professor Yang, my colleague Katherine Miller is eager to visit you in China. She is very interested in K therapy and hopes to promote it in North America. I would like to request a meeting with her.” Griffin requested. This female professor is a leading oncology expert at the MD Anderson Cancer Center.

Yang Ping hesitated for a moment, then said, "Let her come."

A few days later, Yang Ping met Katherine Miller in the conference room. She was around forty years old, with blonde hair tied in a neat ponytail, wearing a simple shirt and trousers, but her eyes were sharp and she exuded the unique temperament of a senior researcher.

“Dr. Miller, welcome.” Yang Ping shook hands with her. “I am Yang Ping.”

“Professor Yang, I’m sorry to take up your valuable time.” Catherine’s Chinese was quite fluent. “I read your team’s paper on the mechanism of action of the K factor and was very inspired. I specifically wanted to ask you some questions in person.”

"Please sit down." Yang Ping gestured for her to sit. "Is it about the application of K therapy?"

“Not only that.” Catherine took a tablet computer out of her briefcase and opened a document. “We have admitted a special group of pancreatic cancer patients at MD Anderson Cancer Center. There are seven of them, all of whom are young women with no family history and no typical risk factors, but their tumors are progressing very rapidly and are resistant to all existing treatments.”

She swiped the screen to show pathological images and genomic data: "We did whole-exome sequencing, transcriptomics, proteomics, and even single-cell sequencing, and found that these tumors have a common feature: they highly express a rare fusion protein, which we named PAC-FUS1."

Yang Ping carefully examined the data and discovered that PAC-FUS1 was generated by the abnormal fusion of two originally unrelated genes: one encoding a cell adhesion molecule and the other encoding an epigenetic modifying enzyme. This fusion resulted in an abnormal protein that possessed both adhesion and chromatin remodeling functions.

“Interestingly,” Catherine continued, “we found in in vitro experiments that PAC-FUS1 can directly bind to and activate multiple growth factor receptors, including EGFR and c-MET, forming an autocrine growth-promoting cycle, which explains why these tumors progress so rapidly.”

"But what problems did you encounter?" Yang Ping asked.

Catherine said, "We tried using inhibitors targeting these receptors, but the effect was short-lived, and the tumors quickly developed bypass activation. What's even stranger is that when we tried treating these patients' tumors with your published Factor K, we found that Factor K was completely ineffective against these tumors."

Yang Ping frowned: "Completely ineffective? Are you sure the experimental conditions were correct?"

“It was repeated three times, with strict controls,” Catherine stated confidently. “Other pancreatic cancers respond as expected to factor K, but these seven samples showed no change. It’s as if their cancer cells don’t have a target that factor K can recognize.”

These words flashed through Yang Ping's mind like a bolt of lightning.

If the PAC-FUS1 fusion protein alters the cancer cells' identification mechanisms, causing them to hide or change that common target, then these tumors will become naturally resistant to K therapy.

However, this also means that PAC-FUS1 itself may become a new and more specific target.

"Have you tried targeting the fusion protein itself?" Yang Ping asked.

“We’ve tried RNA interference and small molecule inhibitors, but the effects have been limited,” Catherine said. “Fusion proteins are located between the cell nucleus and the cell membrane, making them difficult to target. Moreover, they may have multiple functions within the cell, and simple inhibition can trigger complex compensatory responses.”

The conference room fell into a brief silence.

“Dr. Miller, you’ve come at the perfect time.” Yang Ping stood up. “Our team is currently studying a common target in pancreatic cancer, which may be the one you’ve observed that these fusion proteins are missing in tumors. You are welcome to visit our lab.”

Catherine's eyes lit up: "That's exactly what I've been looking for."

In the lab, Yang Ping briefed Catherine on the team's current progress. When Catherine saw the three-dimensional model of the PANC-ID1 complex constructed by Lu Xiaolu, her expression changed from curiosity to shock.

"You've already done this?" she asked incredulously. "It took us two years to purify enough PAC-FUS1 for preliminary crystallography, with a resolution of only 3.8 angstroms. You can see the structural dynamics in situ using cryo-electron tomography?"

"This is Dr. Lu Xiaolu's specialty, and Dr. Griffin gave good advice," Yang Ping explained.

Lu Xiaolu briefly explained the technical details to Catherine, who listened attentively, taking notes and occasionally asking technical questions.

“I have an idea,” Catherine said after listening to the presentation. “If PAC-FUS1 tumors lack the normal PANC-ID1 complex, or if this complex is modified by a fusion protein and its function is altered, then factor K targeting the normal complex will naturally be ineffective. But conversely, PAC-FUS1 itself may present a new identity. If we can design a factor K that recognizes this characteristic, we can specifically target this type of highly malignant tumor.”

“It’s theoretically feasible, but we need to know the exposed epitopes of PAC-FUS1 on the cell surface,” said Song Zimo. “Fusion proteins often generate new antigenic epitopes, which may be ideal targets.”

“We have preliminary mass spectrometry data.” Catherine pulled up another file. “The extracellular portion of PAC-FUS1 mainly comes from the original adhesion molecule, but a new short peptide sequence of about 15 amino acids was generated near the fusion site. This sequence has never been expressed in normal human tissues, and it should be a tumor-specific neoantigen.” Yang Ping carefully examined the sequence: “If this sequence is indeed exposed on the cell surface and is conformationally stable, it is indeed an excellent target, but we need to verify its accessibility. Moreover, I think it could be a supplement to our research. By studying their differences, I can discover more secrets.”

“We can collaborate on validation,” Catherine proposed. “I will provide organoids and cell lines for PAC-FUS1 tumors, and you can use your platform to study their surface antigen profiles. Of course, we do not yet have the research capabilities for K therapy, but we can assist you by providing you with special tumor cell samples.”

"Thank you!" Yang Ping is open to cooperation, provided that the company is independent and masters the core technologies.

Catherine showed great interest in all the projects in the lab, especially when she heard Griffin introduce Zhang Lin’s gesture-breathing research data.

“This reminds me of some observations we’ve made in palliative care,” Catherine said. “Patients with advanced cancer often experience anxiety and difficulty breathing, and we teach them some simple breathing techniques, sometimes combined with hand gestures. Although there’s no systematic research, clinicians generally find it helpful.”

Zhang Lin, standing nearby, felt as if he had found a kindred spirit: "What do you think this mechanism might be?"

“In addition to the attention regulation and neural reflexes you have already discovered, there may also be socio-psychological factors,” Catherine analyzed. “When a person feels helpless, giving them a specific, controllable physical action can reduce anxiety and indirectly improve their physiological state, which is especially evident in cancer patients.”

Yang Ping nodded: "Therefore, Zhang Lin's research may be valuable, revealing potential physiological regulatory mechanisms and providing simple and easy-to-implement intervention methods for symptom management, which may be particularly meaningful in medical environments with limited resources."

Encouraged, Zhang Lin then went on to detail his next planned experiment.

A few days later, MD Anderson Cancer Center airlifted tumor cell samples. Lu Xiaolu and Griffin improved the in-situ structural resolution of the PANC-ID1 complex to 8.5 angstroms by optimizing sample preparation and image processing algorithms. At this resolution, the relative positions and approximate shapes of the various subunits, as well as the charge distribution pattern on the wobbling accessory protein, could be clearly seen.

Meanwhile, the PAC-FUS1 tumor cell line provided by Catherine also arrived. The team used surface proteomics to analyze the cells and found that the fusion-specific short peptide sequence was indeed exposed on the cell surface and was relatively stable.

“There must be some kind of connection between the two targets.” At the project progress meeting, Yang Ping summarized, “Is PAC-FUS1 just PANC-ID1, or is it an expression under certain special circumstances?”

“Their structures are so different, even though they have some similarities,” Catherine said, adding that she had never thought of it that way.

Yang Ping thought for a moment: "We can conduct a comprehensive study on the two types of verification, from structure and function, etc., so that we can find their internal connection. Before we find their connection, we can design K-factors separately with them as targets."

The first step in designing the K factor is to determine the binding mode. Song Ziming and Catherine used computer simulations to predict the most likely conformation of the PAC-FUS1 neoantigen epitope, and then designed hundreds of candidate binding molecules. Instead of traditional antibodies, they designed hybrid structures based on nanobodies and synthetic peptides, which are smaller, more stable, and easier to produce.

After initial screening, twenty candidate molecules with the highest predicted affinity were selected for gene synthesis and prokaryotic expression.

At this crucial stage, an unexpected discovery changed everyone's plans.

One late night, while analyzing a new batch of cryo-electron microscopy data, Lu Xiaolu discovered a previously overlooked phenomenon: on the membrane of PAC-FUS1 tumor cells, not only was the normal PANC-ID1 complex lacking, but an abnormal multi-protein aggregation structure also existed.

He magnified the image and analyzed it carefully. These aggregated structures were formed by the PAC-FUS1 fusion protein as the core, surrounded by a variety of membrane receptors and signal transduction proteins, forming a "signal hub".

“Look here.” The next morning, Lu Xiaolu showed his findings to the team. “PAC-FUS1 not only changes the cell identity, but it also builds an unusual command center on the membrane. EGFR, c-MET, integrins… these receptors are physically pulled together to form a super complex, resulting in continuous and strong activation of downstream signaling pathways.”

Catherine gasped: "This explains why single-target inhibitors are ineffective; inhibiting one receptor allows other receptors to immediately compensate. They are physically bound together, like a multi-headed monster."

“But this also gives us a new opportunity.” Yang Ping stared at the screen. “What if this supercomplex itself is a more significant target? Targeting a single receptor may result in off-target effects, but targeting this tumor-specific complex structure would be much more specific.”

“Moreover,” Lu Xiaolu added, “structurally, PAC-FUS1 is at the core of this complex, with multiple receptors arranged around it. If our K factor can recognize the new antigenic epitope of PAC-FUS1 and also has some kind of cross-linking function, it may be able to disrupt the stability of the entire complex and cut off multiple signaling pathways at once.”

This idea excited everyone. Instead of simply labeling cancer cells for the immune system to eliminate, it directly disrupts the signaling hubs that cancer cells depend on for survival, which is a more proactive attack strategy.

“Designing such a K factor is more difficult,” Song Ziming calmly analyzed. “It needs to have both high affinity recognition and the ability to induce protein disaggregation, which may require the introduction of new functional domains.”

"Are there any precedents for this in nature?" Tang Shun asked.

“Yes.” Catherine suddenly remembered something. “Some bacterial toxins and viral proteins can disrupt the multi-protein complexes of host cells. For example, a domain of diphtheria toxin can induce the dissociation of protein aggregates. Perhaps we can learn from these natural designs.”

With new cell samples, ideas opened up and various possibilities emerged. The team decided to change direction: instead of designing simple marker-type K factor, they designed therapeutic K factor with destructive function.

This is undoubtedly a bolder and riskier goal, but if successful, the results will be even more significant.

Just as the team was fully committed to the new direction, news came from Zhang Lin.

"Professor, you have to take a look at this." Zhang Lin's voice trembled slightly on the phone, whether from excitement or nervousness, it was hard to tell.

Yang Ping thought Zhang Lin had made some major discovery, so he rushed to Zhang Lin's laboratory and found him staring blankly at the computer screen.

"what happened?"

Zhang Lin pointed to the complex data charts on the screen: "I expanded the sample size and found that hand gestures control muscles in the same way. The thumb moves rhythmically from the index finger to the little finger, and the muscles involved in breathing move downwards in a regular pattern. In other words, hand gestures can control neural pathways. I'm certain that Qigong has a certain scientific basis, but it has been mystified and exaggerated. It is very likely a way to regulate the nervous and humoral systems using body movements and intentions, Professor..."

P.S.: Happy New Year everyone! Thank you for your support!