godfather of surgery

Chapter 1307 Fatal Command
Leveraging the network and influence generated by the global promotion of K therapy, large-scale sample collection was carried out worldwide.

Tumor cell samples from major hospitals across China were rapidly sent to the Sanbo Institute. Thanks to the active efforts of Griffin, Robert, Johannesson, August, Mainstein, Takahashi, and others, cryogenic transport boxes bearing special biohazard labels and encrypted barcodes converged on the Sanbo Institute from abroad, from the MD Anderson Cancer Center to European Molecular Biology Laboratories, from the National Cancer Center of Japan to remote research institutes in Australia, like a pilgrimage.

They brought invasive frontal tissues of glioblastoma, circulating tumor cell clusters of triple-negative breast cancer, metastatic lymph nodes of esophageal squamous cell carcinoma, rare biopsy specimens of undifferentiated thyroid carcinoma, and even some difficult-to-classify tumor samples that were hard for even the original institutions to classify. Each sample was accompanied by the most detailed clinicopathological information and preliminary molecular subtyping data possible.

Yang Ping stood in the laboratory, while Song Ziming stood beside him, reporting on the latest progress.

"As of 8:00 AM this morning, 4876 solid tumor samples have been entered into the database and completed initial quality control, covering 92% of the major types of solid tumors and more than 300 rare subtypes in the World Health Organization classification. The high-throughput surface proteomics analysis platform is operating at full speed, and the preliminary antigen profiles of the first batch of 1200 samples have been generated. On Lu Xiaolu's side, the cryo-electron microscopy schedule is already booked for six months ahead. They are optimizing the automated sample preparation and pre-screening process, which has tripled the processing throughput."

Yang Ping nodded slightly: "Samples are not numbers, but keyholes. Each unique tumor uses its surface molecular combination to show us the specific expression pattern of the TIM superfamily in this individual and in this environment. What we are looking for is not commonality, but the grammar of commonality."

As the number of samples increased, Yang Ping became busier, spending almost all his time in the laboratory and not returning home until very late.

During the day, he shuttled between various platforms, discussing the low-resolution contours of abnormal TIM structures on the surface of a sarcoma sample with Lu Xiaolu, arguing with Tang Shun about the parameter settings of the clustering algorithm, and personally checking the data quality of surface protein fluorescent labels.

At night, he immerses himself in his office, where tens of thousands of protein structure prediction maps, interaction networks, and evolutionary tree models flow across the smart screens.

Jiang Jitong would occasionally be called in to help organize data or operate visualization software. He was amazed by Yang Ping's ability to process multi-dimensional information. Yang Ping could simultaneously view the comparison of TIM candidate structures for more than a dozen tumor types and point out that a systematic difference in the angle of a certain loop region might be related to the embryonic origin layer; he could instantly identify a non-coding RNA that might regulate the expression of a group of TIM members in a chaotic gene co-expression network; he could even deduce from clinical prognostic data that a certain TIM conformational variant might confer special tolerance of cancer cells to a hypoxic microenvironment.

Over 80% of solid tumor samples tested positive for surface protein complexes with that characteristic core folding pattern. They resemble different architectural styles built from the same basic structural components within a vast complex. However, how are these components selected by cancer cells? What are the underlying connections between them? Is it merely structural similarity, or do they share some deeper regulatory logic or functional hub?
What kept Yang Ping awake at night was his thoughts about the "key" lineage.

If TIM is the lock and K factor is the key, then how exactly does this key work? The earliest discovery of K factor was entirely accidental. After being injected into the human body, K factor can automatically find its corresponding identification lock. This indicates that under certain conditions, tumor cells can self-secrete K factor or participate in its formation.

Is factor K not just a marker or disruptor? Could it trigger a termination program that already exists within cancer cells but has been deeply suppressed or bypassed?
This thought sent a chill down Yang Ping's spine. If cancer cells themselves carry a self-destruct switch, but are merely shielded by the illusion of identity and abnormal signals maintained by the TIM system, then the essence of treatment might not be an external attack, but rather an internal awakening.

In this sense, the process of K factor treatment for osteosarcoma is actually an awakening process, not an eradication process; it merely awakens the self-destruct program of tumor cells.

This discovery gave Yang Ping a sudden insight, and he focused his attention on three cases with great excitement.

A sample of an extremely rare pediatric soft tissue sarcoma from Northern Europe. For this highly aggressive and almost incurable tumor, factor K showed near-miraculous effects in in vitro experiments, with over 70% of tumor cells undergoing typical apoptotic morphological changes within 48 hours. However, further analysis revealed that this apoptosis did not depend on the classic caspase pathway, but was accompanied by violent oscillations in the mitochondrial membrane potential and an atypical chromatin condensation.

In another advanced melanoma sample that had acquired resistance to immune checkpoint inhibitors, the binding affinity of standard factor K was decreased. However, when a targeted, modified factor K, fine-tuned according to its TIM variant, was used, not only was binding restored, but the tumor cells were unexpectedly resensitized to the original immunotherapy. It appears that factor K binding alters the immune visibility of tumor cells.

Another sample, provided by Catherine's team, consisted of pancreatic cancer organoids that developed early resistance to PAC-FUS1-targeting factor K. The TIM structure of the resistant cells did not disappear, but the surrounding shielding protein network became more complex. However, when using an enhanced factor K variant designed with a transmembrane domain capable of partially penetrating the cell membrane, the PAC-FUS1 fusion protein was observed to be abnormally localized and aggregated within the cells, ultimately being cleared by autophagy.

Three cases, three different TIM variants, and three different approaches to improving the K factor led to three different biological outcomes, all of which went beyond the effects of simple labeling.

Yang Ping imported the data streams from the three reports into a brand-new analytical model. This artificial intelligence model no longer focuses solely on structure, but attempts to integrate dynamic signal flow, energy metabolism state, and epigenetic landscape.

He constructed a simplified theoretical framework: viewing TIM as a "sensor-emitter" integrated module of cancer cell "identity state". This module continuously receives internal and external signals and outputs instructions to maintain the specific survival state of cancer cells.

The K-factor can perhaps be understood as a kind of "forced signal simulator" or "system disruptor." When it combines with TIM, it doesn't simply attach a label, but rather inputs a strong, unnatural signal into the cancer cell's identity control system. This signal may "overload" the system's analytical capabilities, "short-circuit" normal signaling pathways, or accidentally activate the "self-check-cleanup" program deep within the system as a fail-safe mechanism.

"It's like forcibly inputting a contradictory instruction into an AI program that's gone crazy and is self-replicating, but it has a very high priority and can't be processed by its underlying code..." Yang Ping quickly wrote down on an A4 sheet of paper. "The instruction could be 'authentication failed' or 'execute the preset redundancy removal protocol'."

He abruptly stopped pointing. The pre-set cleanup protocol? Yes! That's it.

Yang Ping picked up his phone, his hand trembling, and dialed Xiao Su's number: "Honey, I should be able to find a self-destruct mechanism in tumor cells soon. It has a self-destruct mechanism." Xiao Su was always his loyal listener; when Yang Ping had an inspiration, she was usually the first person he told. Looking at the time, it was already very late. Yang Ping had to go home; he never stayed out overnight, even in the lab.

When he got home, he excitedly "reported" his thoughts to Xiao Su in detail. Xiao Su just listened quietly, her eyes filled with admiration. She nodded from time to time and sometimes asked a few very professional questions.

Before going to sleep, Yang Ping enters the system space to think, which can improve the efficiency of his thinking.

All living organisms possess mechanisms for eliminating abnormal, damaged, or excess cells. Apoptosis, autophagy, pyroptosis… these are the cornerstones of maintaining order in multicellular organisms. Cancer cells become cancer cells precisely because they evade these elimination mechanisms. But what if, in the most primitive programming of cell differentiation and identity establishment, there is a deep, logical link between elimination mechanisms and the identity recognition system itself?
For example, a liver cell must continuously express the "I am a liver cell" identity signal in order to receive the "survival" instruction from the microenvironment; once it loses its identity signal or the signal is incorrect, a pre-programmed elimination procedure will be activated to prevent it from becoming an uncontrollable threat. Cancer cells may deceive the elimination system by continuously and incorrectly overexpressing a hijacked TIM signal, thus disguising themselves as having "legitimate identity."

The K factor, by binding to TIM with high intensity and specificity, may be equivalent to declaring to the system: "This identity signal is forged" or "The signal strength is abnormal, initiate verification." If the binding is strong enough and the scope is critical enough, it may be able to break through the disguise of cancer cells and trigger the "verification-clearance" response hidden in its underlying logic.

This explains why factor K targeting different TIM variants may trigger different downstream effects. Different cancer cell types hijack different TIM members, and their logical linkages with downstream clearance processes may also differ. Some linkages are more direct, such as inducing apoptosis; others require indirect perturbation of other pathways, such as restoring immune visibility; and still others require physical disruption of the abnormal protein itself, such as promoting autophagy.

This idea needs to be validated, and it needs extremely precise validation, as it involves intervening in the most fundamental survival logic of cancer cells.

The next day, Yang Ping turned his attention to several special samples in the sample library.

Those are several extremely rare tumor types known to have very high spontaneous regression rates, including certain neuroblastomas, nephroblastomas, and melanomas. If his conjecture is correct, the TIM system of these tumors may exhibit some kind of "instability" or "link sensitivity" to the clearance process.

“Tang Shun,” Yang Ping answered the phone, “screen all samples for cases with large fluctuations in TIM expression levels or significant negative correlations with apoptosis-related gene expression. Pay special attention to tumor types with reported spontaneous regression. I need their single-cell transcriptome and surface proteome combined analysis data, the more detailed the better.”

“Furthermore,” he added, “inform Lu Xiaolu and Song Ziming to suspend all general screening of new samples and concentrate all high-resolution structural analysis resources on three main targets for in-depth analysis: the TIM structure that efficiently induces apoptosis in pediatric soft tissue sarcoma, especially its transmembrane region and intracellular short tail conformation; the TIM variant in melanoma that can restore immune sensitivity, focusing on its potential proximity relationships with MHC-I molecules or interferon signaling pathway components; and the key epitopes on the PAC-FUS1 resistant variant that undergo autophagy clearance after being attacked by enhanced factor K. We need to find those truly lethal weaknesses or switch regions in the TIM structure.”

Soon, preliminary results began to emerge.

In tumor samples with spontaneous regression potential, Tang Shun's team did indeed discover some interesting patterns: their TIM expression was often less stable, exhibiting heterogeneity in different regions of the same tumor and even between different cells. Furthermore, certain TIM subtypes showed a subtle inverse relationship with a set of genes known as "cell fate checkpoints," including preparatory elements for some pro-apoptotic factors. Single-cell data revealed that cancer cells with the lowest TIM expression or exhibiting atypical conformations often also displayed higher stress levels and a transcriptional profile more inclined towards differentiation or quiescence.

Lu Xiaolu has made a breakthrough. High-resolution structural analysis of childhood sarcoma TIM revealed that its intracellular short tail folds at a unique angle, spatially very close to a protein on the mitochondrial outer membrane involved in a non-classical apoptosis initiation process. Molecular dynamics simulations suggest that when factor K binds tightly to the extracellular portion of TIM, it may transfer the full-length conformation, pulling on the short tail and greatly increasing its probability of contact with the mitochondrial protein, thereby physically triggering the apoptosis switch.

The TIM variant structure of melanoma reveals that a specific glycosylation modification loop is located adjacent to the groove on the cell surface where MHC-I class molecules load peptides. When this loop is occupied by factor K or induced by allosteric changes, it may affect the stability of nearby MHC-I molecules or the efficiency of peptide display, thereby altering the antigen presentation landscape of tumor cells recognized by T cells.

The PAC-FUS1 case is the most complex, but also the most fundamental. The epitope attacked by the modified K factor is located near the linker region of the fusion protein. This region may normally be protected by other proteins or be in a dynamic state. The strong binding and partial internalization of the K factor may expose this region, making it recognized by intracellular quality control mechanisms as "misfolding" or "abnormal aggregation," thus marking it as a target for autophagy clearance.

All three clues seem to point in the same direction: TIM is not merely a static "label," but a dynamic and integrative "signal processing hub." It connects the inside and outside of the cell, and its state directly affects the cell's core fate decisions—survival, death, visibility, or concealment.

Yang Ping pieced these fragments together, and a more complete picture began to emerge:
In the early programming of life, the establishment and maintenance of cellular identity requires a sophisticated recognition and feedback system, the prototype of the primitive TIM system. This system ensures that cells are in the correct location, express the correct function, and are eliminated when they lose their location or malfunction. This may be one of the underlying logics for maintaining tissue order in multicellular life.

Under evolutionary pressure, cancer cells hijacked and modified certain components of this system, turning them into "protective shields" for their abnormal survival. They used TIM to send fake "everything is normal" signals to suppress internal cleansing processes and to engage in self-serving dialogue with the microenvironment.

The K factor, acting as a highly specific "external decoder and disruptor," can send a strong "system anomaly" alarm by precisely binding to TIM. If this alarm is strong enough and the attack point is critical enough—for example, by directly interfering with signal output, destroying key structures, or exposing intrinsic defects—it may overwhelm the cancer cells' disguise and trigger various clearance mechanisms that remain in their underlying programming or are connected to the TIM system logic, initiating apoptosis, immune exposure, autophagy, and especially the apoptosis program.

This is not a single killing mechanism, but a multi-path "forced system reset or shutdown" strategy based on vulnerabilities in the cancer cells' own "operating system".

This understanding has transformed cancer treatment from "finding specific targets to attack" to "understanding system logic and sending lethal commands."

(End of this chapter)