A genius? I just love studying.

Chapter 313 Junior Brother Chen is awesome

After finishing his meal, Chen Hui cleaned up the trash, put it in the trash can, and returned to his computer.

While eating, he had just found a new inspiration after clearing his mind. He realized that this was biology, this was medicine, and it could not be driven by pure mathematics alone. Biological constraints had to be added to the model!
Logged onto a professional academic paper website, Chen Hui began searching for papers related to protein-protein interaction databases and known signaling pathway maps. He had some prior knowledge of this topic, but had not studied it in depth.

As time went by, Chen Hui, like a thirsty sponge, frantically absorbed all knowledge.

A week later, with everything in place, Chen Hui began to further improve his model. Instead of applying it directly, he transformed this knowledge into weak prior information, namely, which proteins are more likely to interact with each other. Based on known complexes, domain similarities, etc., he provided some fuzzy, probabilistic guidance for the model.

Then Chen Hui used the Bayesian network machine learning method, which is particularly suitable for inferring causal networks from data and can easily incorporate the weak prior information he collected as constraints.

The new model was completed quickly.

After running the new model, a preliminary, probabilistic network graph was obtained.

The diagram points to a previously overlooked protein kinase called PKCδ, which may be at the heart of this new pathway.

Chen Hui smiled happily. After so many busy days, he finally achieved a pretty good result.

However, Chen Hui soon frowned. In the model, the connection between PKCδ and the upstream was still unclear. The current information was simply not enough to provide sufficient confidence.

We've made progress, but it's not enough!

Chen Hui took a deep breath. He was already used to such arduous research and felt not discouraged at all, but rather full of fighting spirit.

This time, he spent three whole days, but still couldn't come up with a better idea.

The research appears to have reached a stalemate.

Song Chaoming also came a few times during this period. After all, Chen Hui had been with their team for almost half a month, but there had been no progress, so he naturally had to come and see.

He was initially a little apprehensive, but after seeing Chen Hui's second version of the model, he was so excited that he almost danced in the conference room.

However, he still approved of Chen Hui's rigorous attitude.

Unlike Tang Jian, he has already achieved great success, and even if he publishes another paper in Nature or Science, it will not bring him much benefit, so he is not as obsessed with publishing papers.

They are researching tumors, and the final research results are meant to be used on patients. They can't simply use a seemingly perfect result to replace the real situation.

Even if the drug is tested on animals in advance, no one can say for sure what terrible consequences might occur in the end, so we naturally need to be extremely cautious.

Moreover, Chen Hui has already achieved such a surprising result in just half a month, so he doesn't mind waiting a few more months.

call!
Let out a long breath, Chen Hui looked away from the screen, and cleared his mind for a moment.

He did indeed encounter a problem.

A few seconds later, Chen Hui's gaze regained its firmness. He looked at the computer screen again, moved the mouse, and reopened the historical research data of Song Chaoming's team.

Since it's dark ahead and we can't find a way out for now, let's look back and look for possible clues from this data.

Another week has passed. This time, Chen Hui examined the data in a more meticulous way, spending more time than before, but the inspiration he wanted still hadn't arrived.

That's how scientific research is. Even if you spend a lot of time and energy and put in a lot of effort, you may not necessarily achieve results. Sometimes, a sudden idea might lead to a great discovery.

At two o'clock in the morning, Chen Hui slowly moved the mouse in the conference room, his sharp eyes constantly scanning the complex data.

Time passes little by little.

It was already 2:50.

Chen Hui looked away; he was getting ready to sleep.

Since junior high school, his sleep schedule has been very regular. Unless there is an emergency, he goes to bed at three in the morning and gets up at six in the morning.

It is his regular sleep that gives him a healthy body and allows him to maintain his energy for studying and research.

Suddenly, Chen Hui narrowed his eyes.

He noticed a detail in the experimental records that everyone had overlooked: the mass spectrometry data were samples taken at different time points: 0h, 1h, 6h, and 24h!
Previous analyses had subconsciously merged these data, attempting to find a static network.

However, it is clear that the activation of signaling pathways is a dynamic process!
Just like watching a passing game, you have to watch the video replay, not look at a group photo, to know who passed to whom.

A flash of inspiration appeared, followed by a surge of countless flashes of inspiration.

It was as if the paper covering the spring water had been knocked away, and then the golden spring gushed forth from the ground!
Chen Hui immediately turned to dynamic Bayesian networks and time series analysis, connecting data from different time points according to their inherent temporal relationships.

He built a model to track the trajectory of phosphorylation levels of each signaling protein over time.

By analyzing the temporal sequence and covariance among these trajectories, the inference of causal relationships becomes clearer than ever before. If the activation of protein A consistently occurs before protein B, then the probability that A is the cause of B is greatly increased.

The fog instantly dissipated!

The dynamic model clearly shows that a specific EGFR mutant first rapidly recruits and activates an adapter protein, which then unexpectedly activates PKCδ at a specific time point. PKCδ then bypasses the classic RAS protein, directly phosphorylates and activates the downstream RAF isoenzyme, thereby taking a shortcut to drive the entire proliferative pathway.

Chen Hui quickly found a high-confidence non-classical pathway model that had been validated by dynamic time series data: mutation EGFR->Gab1->PKCδ->CRAF->MEK->ERK.

He also used this model to predict several key nodes. If PKCδ is inhibited, it should be able to specifically block this non-classical pathway and reverse drug resistance. He even predicted the order and approximate magnitude of the decrease in phosphorylation levels of downstream proteins after inhibition.

……

At eight o'clock in the morning, Tang Jian arrived at the laboratory on time, carrying fresh soy milk and fried dough sticks to the small conference room.

Squeak,

Before Tang Jian could even enter the conference room, the door was pushed open, and Chen Hui walked out.

Tang Jian stood there, stunned, his eyes widening in an instant.

Chen Hui has been in the conference room for more than a month and has never come out. Does his coming out now mean that the model framework has been successfully constructed?

"Notify Professor Song to prepare for the verification!"

Chen Hui didn't keep Tang Jian in suspense. He took the soy milk and fried dough sticks from Tang Jian and began to enjoy them heartily.

Half past eight,
Huaxia Academy of Medical Sciences, National Key Tumor Research Laboratory
The team of twenty-three people gathered together in the large conference room.

"Really? Did he really finish building the model?"

Even now, apart from Tang Jian, the other junior brothers and sisters still hold a skeptical attitude.

"Such a grand display, it can't be fake, right?"

Another junior student said he couldn't imagine the extent of the trouble that undergraduate student would cause if he were lying. "If it were true..."

One of the junior disciples' eyes gleamed with a sharp light. "Then aren't we just lucky to have caught up with this opportunity?"

They have been conducting this research for three years and naturally know its value. If their conjecture can be confirmed, the result will be world-class, and they will become the absolute authorities in this field.

"Stop dreaming, let's see the verification results first..."

"Alright, everyone has seen the simulation results of the model. Next, we need to use Western blotting technology to confirm the target."

Song Chaoming stood at the front of the conference room, clapped his hands, and waited until the conference room quieted down before speaking.

They needed to replicate the most critical starting point of Chen Hui's model to confirm that in their specific EGFR mutant cell lines, the phosphorylation level of PKCδ did indeed increase abnormally after drug administration, and the timing matched the prediction.

This is the foundation of everything; only after the target has been identified can they proceed to the next stage of the experiment.

Soon, Song Chaoming arranged the experimental tasks, and everyone dispersed, put on their lab coats, and entered the laboratory. Although they still had some doubts, they were also eager to see the final verification results.

Unfortunately, biological experiments differ from other experiments in that they require time to develop and cannot be rushed.

The experiment proceeded in a tense but orderly manner, with the incubator running day and night, and the laboratory lights often on late into the night.

The Western blot results didn't come back until three days later.
When the developed film was taken out of the darkroom, the lab technician in charge practically ran to give it to Song Chaoming.

The results were crystal clear: at 1 hour and 6 hours after drug administration, the phosphorylation bands of PKCδ were indeed significantly more concentrated than those in the control group! The first step of the model's prediction was perfectly confirmed!

A small cheer erupted in the laboratory, and everyone's gaze towards Chen Hui changed. Some felt guilty for their previous doubts, while others were filled with fervent admiration for Chen Hui's astonishing abilities.

"Junior Brother Chen is awesome!"

Suddenly, one of the junior disciples shouted excitedly.

"Junior Brother Chen is awesome!"

Soon, such cheers filled the laboratory.

A relieved smile appeared on Song Chaoming's face. His key laboratory hadn't experienced such enthusiastic cheers in a long time.

"Okay, this is just the first step. The most crucial part is yet to come."

After waiting a few minutes, until everyone had vented their excitement, Song Chaoming spoke again.

Next, they need to conduct gain-of-function/loss-of-function experiments. First, they need to design and synthesize siRNA targeting the PKCδ gene, transfect it into cancer cells, and specifically silence the expression of PKCδ.

Cells were treated at different concentrations using a known, relatively specific PKCδ inhibitor, such as Rottlerin or an analogue.

We used CCK-8 or MTT assays to examine changes in cancer cell proliferation under the conditions of targeted therapy alone, inhibition of PKCδ alone, and a combination of both.

According to Chen Hui's model prediction, the combination group should exhibit a significant synergistic inhibitory effect.

The next step is to conduct long-term observation to see if the combination therapy completely destroys the ability of cancer cells to form colonies under long-term effects.

After the above treatment was applied, the phosphorylation levels of the key downstream proteins CRAF, MEK, and ERK predicted by Chen Hui were detected again using Western blotting or phosphorylation antibody microarray.

According to model predictions, inhibiting PKCδ should significantly reduce the phosphorylation levels of these downstream proteins, demonstrating that the pathway was successfully blocked.

Soon, Song Chaoming led his team to develop a follow-up verification plan.

Everyone threw themselves into the following verification experiments with high morale.

The next day, siRNA transfection was completed, and inhibitors were added. The cells continued to culture under their respective treatment conditions. Everyone carefully watched the culture plates, as if they were holding the answer that would determine their fate.

On the fifth day, the results of the cell viability test came out first. Tang Jian processed the data into charts and printed them out, his hands trembling slightly.

The chart shows that when osimertinib is used alone, cell viability decreases, but cell death does not occur, confirming drug resistance.

Using PKCδ inhibitors alone has only a slight impact on cell viability.

However, when the two were used together, cell vitality experienced a precipitous drop!

The inhibition rate far exceeded the sum of the individual effects of the two, indicating a strong synergistic effect!

"It's a success! Teacher! Look!" Tang Jian excitedly pointed at the chart. Song Chaoming grabbed the drawing, his eyes fixed on the curve representing the connection, his face flushed with excitement, and he murmured, "It matches...it matches perfectly!"

Chen Hui breathed a sigh of relief; it turned out he was right!
The results came in the following days, and each step perfectly confirmed Chen Hui's prediction. The control group and the single-drug group could still form cell colonies of different sizes, while the culture plates of the combination group were almost completely clean, which meant that the proliferative potential of cancer cells had been completely eradicated.

Finally, a mechanism backtracking Western blotting was performed. The results showed that after suppressing PKCδ, the signal strengths of downstream p-CRAF, p-MEK, and p-ERK were indeed significantly weakened or even disappeared, as if the gates had been closed.

The signal flow of this non-classical pathway was clearly visualized, and it was completely cut off from the source to the downstream.

Holding all the experimental data reports, the flawless verification report, Song Chaoming stood in the center of the laboratory, his hands trembling slightly with excitement. He looked around at his equally excited and relieved team members.

“We…we succeeded!” His voice was initially choked with emotion, but then became loud and powerful. “Five months! The problem that had been holding us back for five months is solved! Not only solved, but we also discovered a completely new and important drug resistance mechanism!”

He waved the data chart in his hand, "Chen Fei's model is 100% accurate! From the target to the timing, to the function, to the mechanism, every step is predicted with unparalleled precision! This is not luck, this is... this is true skill!"

An unprecedented cheer and applause erupted in the laboratory, mixed with exclamations of relief at the complete release of the pressure that had accumulated over the past few years. Some people even jumped up excitedly, gesturing wildly in the laboratory, unable to contain their excitement.

Song Chaoming immediately took out his phone, walked to the window, and made his first call to Professor Liu, almost shouting, "Old Liu! That Chen Hui you introduced... he's a genius! Absolutely! He solved it! He solved it perfectly!"

Liu Jishou was also somewhat excited. He hadn't expected Chen Hui to solve Song Chaoming's problem so quickly. Of course, this was because he didn't fully understand the importance of Song Chaoming's achievement.

For his second call, Song Chaoming didn't hesitate to call Chen Hui himself.

"Chen Fei!" His tone was filled with barely suppressed excitement and admiration. "The verification results are in... perfect! All the predictions matched perfectly! You've opened a whole new door for us!"

On the other end of the phone, Chen Hui's voice remained calm, simply replying, "That's good, Professor Song. Send me a copy of the data; it will be very helpful for optimizing my model."

After fully understanding Song Chaoming's thinking, Chen Hui knew that this achievement could only be considered an advancement in tumor research and could not completely solve cancer.

Because such non-classical pathways are difficult to enumerate, and the symptoms of each cancer patient are not exactly the same, it is very likely that there will be a thousand classic pathways for a thousand lung cancers.

This is just a small step, nothing to be overjoyed about.

Song Chaoming put down the phone, looked out the window, and felt a surge of emotions.

He understood that he was witnessing not only the solution to a technical problem, but also the arrival of a brand-new and powerful scientific research paradigm, and the person who brought about this change was such a young foreign aid worker.

From that moment on, Chen Hui's name carried a heavy weight in his heart.

(End of this chapter)