Day: August 31, 2025

I’ve always been fascinated by antibodies. My journey began in 2000, when I first took an undergraduate immunology class. During graduate school in Medical Biotechnology, I dove deeper—advanced immunology in 2001, psychoneuroimmunology in 2002—researching NKT cells and CD1d in autoimmune diseases. Back then, my curiosity was pure: I just wanted to understand how things worked. Papers, grants, and impact factors? I didn’t think about those. Honestly, even now, grant writing still feels like a mountain to climb!

Until 2018, during my third postdoc, I never actively pursued grants. I was fortunate to be in well-funded labs, free to follow my interests, attend meetings, and write papers when inspiration struck. That freedom was exhilarating. I often chose research topics my supervisors weren’t interested in—at least initially—giving me the joy of discovery.

But freedom has a cost. By the time I tried to apply for my own grant, it felt late. I wrote one in 2018, only to have my name removed by my PIs and replaced with a colleague’s. They told me it would increase our chances of funding. I also learned a hard lesson: in both academia and industry, even great data isn’t always shareable due to patents. At the end of the day, the only guaranteed rewards were a paycheck and the sheer pleasure of exploring science.

Sometimes I wonder if I should have pursued a Ph.D. in immunology instead of neurobiology. I missed a lot of immunology along the way. Still, I wouldn’t trade my journey—it shaped the scientist I am today.

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Generating Antibodies: My Hands-On Experience

If you’ve worked in biology or medicine, you know antibodies are everywhere. They’re essential for research and diagnostics, from simple antibody staining to generating completely new reagents.

During my Ph.D., I generated antibodies both in-house and through companies. I provided expression constructs, sometimes purified proteins, and worked with animals like mice or ferrets. It took time, patience, and more than a few failed attempts—especially for antibodies against certain domains. For instance, when generating pan-antibodies against protocadherin 7, we eventually produced polyclonal antibodies, but monoclonal antibodies just didn’t cooperate.

Fast forward to 2020–2021: antibody engineering has advanced tremendously. I created numerous AAV constructs, including Fab and scFv, analyzing backbones, VH, VL, CDRs in detail. Companies sometimes tweaked CDRs sequences, either randomly or with AI. Even Fc regions required careful attention, as they could influence adverse effects in the case of Fc-fused proteins and full antibody drugs. To generate AAV constructs, all other parts, such as promoter regions, signal peptides, linkers, polyA, WPRE, etc., should be considered. The next steps are to check whether the antibody-based fragments are secreted and work properly by Western blots and ELISA. Of course, in the case of AAV constructs, we should check AAV property and yields and have AAV first.

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Fc and Fab: The Power of Two

Antibodies have two main regions: Fab and Fc.

• Fab or variable regions bind to antigens
  
• Fc, often called the “effector arm or tail,” performs critical functions:
  
  1. Cell-mediated and humoral immune activation: Fc binds Fc receptors on macrophages, neutrophils, NK cells, and dendritic cells and leads to ADCC (antibody-dependent cellular cytotoxicity) and ADCP (antibody-dependent cellular phagocytosis).
     
  2. Complement system activation: Fc triggers pathogen lysis, opsonization, and inflammation.
     
  3. Half-life regulation: Fc binds neonatal Fc receptor (FcRn) in endothelial cells, protecting antibodies from degradation.
     
  4. Maternal-fetal transfer: IgG Fc interacts with FcRn in the placenta, passing immunity to the fetus.
     

When designing therapeutic antibodies, deciding whether to keep, engineer, or remove Fc is crucial. Fab fragments penetrate tissues better but have shorter half-lives. Fc is often necessary for cancer therapies, whereas autoimmune or blocking therapeutics benefit from Fc engineering to avoid harming self-tissues.

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A Look at Therapeutic Antibodies

Here’s an overview of some major monoclonal antibody drugs and their Fc strategies:

Drug	Target	Indication	Fc Strategy	Engineering / Mutations
Rituximab	CD20	B-cell lymphoma, RA	Active Fc → ADCC + CDC	None
Trastuzumab	HER2	HER2+ breast & gastric cancer	Active Fc → ADCC	None
Adalimumab	TNF-α	RA, Crohn’s, psoriasis	Neutralizing	None
Cetuximab	EGFR	Colorectal & head/neck cancer	Active Fc → ADCC	None
Nivolumab	PD-1	Melanoma, NSCLC	Fc-silent → avoids killing T cells	IgG4 backbone + S228P
Pembrolizumab	PD-1	Similar	Fc-silent	IgG4 backbone + S228P
Omalizumab	IgE	Severe asthma, urticaria	Fc engineered to avoid mast cell activation	IgG1 backbone; avoids C1q binding
Bevacizumab	VEGF-A	Colorectal cancer, AMD	Neutralizing; Fc not critical	Wild-type IgG1

Key patterns:

• Cancer drugs keep Fc active to kill tumor cells.
  
• Checkpoint inhibitors silence Fc to avoid killing PD-1+ T cells.
  
• Anti-cytokine drugs have no effector function, but increase half-life by FcRn recycling.
  
• Anti-IgE drugs engineer Fc to prevent dangerous immune activation.
  

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Fc-Free Antibodies: A Growing Field

Fc-free antibody fragments are also gaining attention. As of August 27, 2025:

Status	Count	%
FDA-approved	15	27%
Terminated / Withdrawn	10	18%
Under Clinical Development	26	47%
Regulatory review	4	7%

Even though Fc can trigger strong immune responses, careful control – through dosing or engineering – can make it highly beneficial. Fc-free fragments face challenges like short half-life or lack of effector function, explaining why some have been terminated.

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Antibody research is a perfect blend of biology, engineering, and clinical innovation. It’s a field full of stories – both successes and failures – that teach us how to translate basic science into therapies. 

I’ve recently started reading again a book on therapeutic antibody engineering (2012), and I plan to share insights and reflections here from time to time.